diff --git a/Modules/Segmentation/Algorithms/mitkCreateDistanceImageFromSurfaceFilter.cpp b/Modules/Segmentation/Algorithms/mitkCreateDistanceImageFromSurfaceFilter.cpp index 33e5a77d04..22f8aaa001 100644 --- a/Modules/Segmentation/Algorithms/mitkCreateDistanceImageFromSurfaceFilter.cpp +++ b/Modules/Segmentation/Algorithms/mitkCreateDistanceImageFromSurfaceFilter.cpp @@ -1,588 +1,585 @@ /*=================================================================== 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 "mitkCreateDistanceImageFromSurfaceFilter.h" mitk::CreateDistanceImageFromSurfaceFilter::CreateDistanceImageFromSurfaceFilter() { m_DistanceImageVolume = 50000; this->m_UseProgressBar = false; this->m_ProgressStepSize = 5; mitk::Image::Pointer output = mitk::Image::New(); this->SetNthOutput(0, output.GetPointer()); } mitk::CreateDistanceImageFromSurfaceFilter::~CreateDistanceImageFromSurfaceFilter() { } void mitk::CreateDistanceImageFromSurfaceFilter::GenerateData() { //First of all we have to build the equation-system from the existing contour-edge-points this->CreateSolutionMatrixAndFunctionValues(); //Then we solve the equation-system via QR - decomposition. The interpolation weights are obtained in that way vnl_qr solver (m_SolutionMatrix); m_Weights = solver.solve(m_FunctionValues); //Setting progressbar if (this->m_UseProgressBar) mitk::ProgressBar::GetInstance()->Progress(2); //The last step is to create the distance map with the interpolated distance function this->CreateDistanceImage(); m_Centers.clear(); m_FunctionValues.clear(); m_Normals.clear(); m_Weights.clear(); m_SolutionMatrix.clear(); //Setting progressbar if (this->m_UseProgressBar) mitk::ProgressBar::GetInstance()->Progress(3); } void mitk::CreateDistanceImageFromSurfaceFilter::CreateSolutionMatrixAndFunctionValues() { unsigned int numberOfInputs = this->GetNumberOfIndexedInputs(); if (numberOfInputs == 0) { MITK_ERROR << "mitk::CreateDistanceImageFromSurfaceFilter: No input available. Please set an input!" << std::endl; itkExceptionMacro("mitk::CreateDistanceImageFromSurfaceFilter: No input available. Please set an input!"); return; } //First of all we have to extract the nomals and the surface points. //Duplicated points can be eliminated Surface* currentSurface; vtkSmartPointer polyData; vtkSmartPointer currentCellNormals; vtkSmartPointer existingPolys; vtkSmartPointer existingPoints; double p[3]; PointType currentPoint; PointType normal; for (unsigned int i = 0; i < numberOfInputs; i++) { currentSurface = const_cast( this->GetInput(i) ); polyData = currentSurface->GetVtkPolyData(); if (polyData->GetNumberOfPolys() == 0) { MITK_INFO << "mitk::CreateDistanceImageFromSurfaceFilter: No input-polygons available. Please be sure the input surface consists of polygons!" << std::endl; } currentCellNormals = vtkDoubleArray::SafeDownCast(polyData->GetCellData()->GetNormals()); existingPolys = polyData->GetPolys(); 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++ ) { existingPoints->GetPoint(cell[j], p); currentPoint.copy_in(p); int count = std::count(m_Centers.begin() ,m_Centers.end(),currentPoint); if (count == 0) { double currentNormal[3]; currentCellNormals->GetTuple(cell[j], currentNormal); normal.copy_in(currentNormal); m_Normals.push_back(normal); m_Centers.push_back(currentPoint); } }//end for all points }//end for all cells }//end for all outputs //For we can now calculate the exact size of the centers we initialize the data structures unsigned int numberOfCenters = m_Centers.size(); m_Centers.reserve(numberOfCenters*3); m_FunctionValues.set_size(numberOfCenters*3); m_FunctionValues.fill(0); //Create inner points for (unsigned int i = 0; i < numberOfCenters; i++) { currentPoint = m_Centers.at(i); normal = m_Normals.at(i); currentPoint[0] = currentPoint[0] - normal[0]; currentPoint[1] = currentPoint[1] - normal[1]; currentPoint[2] = currentPoint[2] - normal[2]; m_Centers.push_back(currentPoint); m_FunctionValues.put(numberOfCenters+i, -1); } //Create outer points for (unsigned int i = 0; i < numberOfCenters; i++) { currentPoint = m_Centers.at(i); normal = m_Normals.at(i); currentPoint[0] = currentPoint[0] + normal[0]; currentPoint[1] = currentPoint[1] + normal[1]; currentPoint[2] = currentPoint[2] + normal[2]; m_Centers.push_back(currentPoint); m_FunctionValues.put(numberOfCenters*2+i, 1); } //Now we have created all centers and all function values. Next step is to create the solution matrix numberOfCenters = m_Centers.size(); m_SolutionMatrix.set_size(numberOfCenters, numberOfCenters); m_Weights.set_size(numberOfCenters); PointType p1; PointType p2; double norm; for (unsigned int i = 0; i < numberOfCenters; i++) { for (unsigned int j = 0; j < numberOfCenters; j++) { //Calculate the RBF value. Currently using Phi(r) = r with r is the euclidian distance between two points p1 = m_Centers.at(i); p2 = m_Centers.at(j); p1 = p1 - p2; norm = p1.two_norm(); m_SolutionMatrix(i,j) = norm; } } } void mitk::CreateDistanceImageFromSurfaceFilter::CreateDistanceImage() { DistanceImageType::Pointer distanceImg = DistanceImageType::New(); //Determin the bounding box of the delineated contours double xmin = m_Centers.at(0)[0]; double ymin = m_Centers.at(0)[1]; double zmin = m_Centers.at(0)[2]; double xmax = m_Centers.at(0)[0]; double ymax = m_Centers.at(0)[1]; double zmax = m_Centers.at(0)[2]; for (unsigned int i = 1; i < m_Centers.size(); i++) { if (xmin > m_Centers.at(i)[0]) { xmin = m_Centers.at(i)[0]; } if (ymin > m_Centers.at(i)[1]) { ymin = m_Centers.at(i)[1]; } if (zmin > m_Centers.at(i)[2]) { zmin = m_Centers.at(i)[2]; } if (xmax < m_Centers.at(i)[0]) { xmax = m_Centers.at(i)[0]; } if (ymax < m_Centers.at(i)[1]) { ymax = m_Centers.at(i)[1]; } if (zmax < m_Centers.at(i)[2]) { zmax = m_Centers.at(i)[2]; } } Vector3D extentMM; extentMM[0] = xmax - xmin + 5; extentMM[1] = ymax - ymin + 5; extentMM[2] = zmax - zmin + 5; //Shifting the distance image's offest to achieve an exact distance calculation xmin = xmin - 5; ymin = ymin - 5; zmin = zmin - 5; /* Now create an empty distance image. The create image will always have the same size, independent from the original image (e.g. always consists of 500000 pixels) and will have an isotropic spacing. The spacing is calculated like the following: The image's volume = 500000 Pixels = extentX*spacing*extentY*spacing*extentZ*spacing So the spacing is: spacing = ( 500000 / extentX*extentY*extentZ )^(1/3) */ double basis = (extentMM[0]*extentMM[1]*extentMM[2]) / m_DistanceImageVolume; double exponent = 1.0/3.0; double distImgSpacing = pow(basis, exponent); int tempSpacing = (distImgSpacing+0.05)*10; m_DistanceImageSpacing = (double)tempSpacing/10.0; unsigned int numberOfXPixel = extentMM[0] / m_DistanceImageSpacing; unsigned int numberOfYPixel = extentMM[1] / m_DistanceImageSpacing; unsigned int numberOfZPixel = extentMM[2] / m_DistanceImageSpacing; DistanceImageType::SizeType size; //Increase the distance image's size a little bit to achieve an exact distance calculation size[0] = numberOfXPixel + 5; size[1] = numberOfYPixel + 5; size[2] = numberOfZPixel + 5; DistanceImageType::IndexType start; start[0] = 0; start[1] = 0; start[2] = 0; DistanceImageType::RegionType lpRegion; lpRegion.SetSize(size); lpRegion.SetIndex(start); distanceImg->SetRegions( lpRegion ); distanceImg->SetSpacing( m_DistanceImageSpacing ); distanceImg->Allocate(); //First of all the image is initialized with the value 10 for each pixel distanceImg->FillBuffer(10); /* Now we must caculate the distance for each pixel. But instead of calculating the distance value for all of the image's pixels we proceed similar to the region growing algorithm: 1. Take the first pixel from the narrowband_point_list and calculate the distance for each neighbor (6er) 2. If the current index's distance value is below a certain threshold push it into the list 3. Next iteration take the next index from the list and start with 1. again This is done until the narrowband_point_list is empty. */ std::queue narrowbandPoints; PointType currentPoint = m_Centers.at(0); double distance = this->CalculateDistanceValue(currentPoint); DistanceImageType::IndexType currentIndex; currentIndex[0] = ( currentPoint[0]-xmin ) / m_DistanceImageSpacing; currentIndex[1] = ( currentPoint[1]-ymin ) / m_DistanceImageSpacing; currentIndex[2] = ( currentPoint[2]-zmin ) / m_DistanceImageSpacing; narrowbandPoints.push(currentIndex); distanceImg->SetPixel(currentIndex, distance); NeighborhoodImageIterator::RadiusType radius; radius.Fill(1); NeighborhoodImageIterator nIt(radius, distanceImg, distanceImg->GetLargestPossibleRegion()); unsigned int relativeNbIdx[] = {4, 10, 12, 14, 16, 22}; bool isInBounds = false; while ( !narrowbandPoints.empty() ) { nIt.SetLocation(narrowbandPoints.front()); narrowbandPoints.pop(); for (int i = 0; i < 6; i++) { nIt.GetPixel(relativeNbIdx[i], isInBounds); if( isInBounds && nIt.GetPixel(relativeNbIdx[i]) == 10) { currentIndex = nIt.GetIndex(relativeNbIdx[i]); currentPoint[0] = currentIndex[0]*m_DistanceImageSpacing + xmin; currentPoint[1] = currentIndex[1]*m_DistanceImageSpacing + ymin; currentPoint[2] = currentIndex[2]*m_DistanceImageSpacing + zmin; distance = this->CalculateDistanceValue(currentPoint); if ( abs(distance) <= m_DistanceImageSpacing ) { nIt.SetPixel(relativeNbIdx[i], distance); narrowbandPoints.push(currentIndex); } } } } - ImageIterator imgRegionIterator (distanceImg, distanceImg->GetLargestPossibleRegion()); - imgRegionIterator.GoToBegin(); - // Fist we set the border slices of the image to value 1000 so that we can perform a // region growing afterwards starting from the middle of the image DistanceImageType::SizeType reqSize; reqSize[0] = distanceImg->GetLargestPossibleRegion().GetSize()[0]; reqSize[1] = distanceImg->GetLargestPossibleRegion().GetSize()[1]; reqSize[2] = 1; DistanceImageType::IndexType reqStart; reqStart[0] = 0; reqStart[1] = 0; reqStart[2] = 0; DistanceImageType::RegionType reqRegion; reqRegion.SetSize(reqSize); reqRegion.SetIndex(reqStart); this->FillImageRegion(reqRegion, 1000, distanceImg); reqStart[0] = 0; reqStart[1] = 0; reqStart[2] = distanceImg->GetLargestPossibleRegion().GetSize()[2]-1; reqRegion.SetIndex(reqStart); this->FillImageRegion(reqRegion, 1000, distanceImg); reqSize[0] = 1; reqSize[1] = distanceImg->GetLargestPossibleRegion().GetSize()[1]; reqSize[2] = distanceImg->GetLargestPossibleRegion().GetSize()[2];; reqStart[0] = 0; reqStart[1] = 0; reqStart[2] = 0; reqRegion.SetSize(reqSize); reqRegion.SetIndex(reqStart); this->FillImageRegion(reqRegion, 1000, distanceImg); reqStart[0] = distanceImg->GetLargestPossibleRegion().GetSize()[0]-1; reqStart[1] = 0; reqStart[2] = 0; reqRegion.SetIndex(reqStart); this->FillImageRegion(reqRegion, 1000, distanceImg); reqSize[0] = distanceImg->GetLargestPossibleRegion().GetSize()[0]; reqSize[1] = 1; reqSize[2] = distanceImg->GetLargestPossibleRegion().GetSize()[2];; reqStart[0] = 0; reqStart[1] = 0; reqStart[2] = 0; reqRegion.SetSize(reqSize); reqRegion.SetIndex(reqStart); this->FillImageRegion(reqRegion, 1000, distanceImg); reqStart[0] = 0; reqStart[1] = distanceImg->GetLargestPossibleRegion().GetSize()[1]-1; reqStart[2] = 0; reqRegion.SetIndex(reqStart); this->FillImageRegion(reqRegion, 1000, distanceImg); // Now we make some kind of region growing from the middle of the image to set all // inner pixels to -10. In this way we assure to extract a valid surface NeighborhoodImageIterator nIt2(radius, distanceImg, distanceImg->GetLargestPossibleRegion()); currentIndex[0] = distanceImg->GetLargestPossibleRegion().GetSize()[0]*0.5; currentIndex[1] = distanceImg->GetLargestPossibleRegion().GetSize()[1]*0.5; currentIndex[2] = distanceImg->GetLargestPossibleRegion().GetSize()[2]*0.5; narrowbandPoints.push(currentIndex); distanceImg->SetPixel(currentIndex, -10); while ( !narrowbandPoints.empty() ) { nIt2.SetLocation(narrowbandPoints.front()); narrowbandPoints.pop(); for (int i = 0; i < 6; i++) { if( nIt2.GetPixel(relativeNbIdx[i]) == 10) { currentIndex = nIt2.GetIndex(relativeNbIdx[i]); nIt2.SetPixel(relativeNbIdx[i], -10); narrowbandPoints.push(currentIndex); } } } Image::Pointer resultImage = this->GetOutput(); Point3D origin; origin[0] = xmin; origin[1] = ymin; origin[2] = zmin; CastToMitkImage(distanceImg, resultImage); resultImage->GetGeometry()->SetOrigin(origin); } void mitk::CreateDistanceImageFromSurfaceFilter::FillImageRegion(DistanceImageType::RegionType reqRegion, DistanceImageType::PixelType pixelValue, DistanceImageType::Pointer image) { image->SetRequestedRegion(reqRegion); ImageIterator it (image, image->GetRequestedRegion()); while (!it.IsAtEnd()) { it.Set(pixelValue); ++it; } } double mitk::CreateDistanceImageFromSurfaceFilter::CalculateDistanceValue(PointType p) { double distanceValue (0); PointType p1; PointType p2; double norm; for (unsigned int i = 0; i < m_Centers.size(); i++) { p1 = m_Centers.at(i); p2 = p-p1; norm = p2.two_norm(); distanceValue = distanceValue + norm*m_Weights.get(i); } return distanceValue; } void mitk::CreateDistanceImageFromSurfaceFilter::GenerateOutputInformation() { } void mitk::CreateDistanceImageFromSurfaceFilter::PrintEquationSystem() { std::ofstream esfile; esfile.open("C:/Users/fetzer/Desktop/equationSystem/es.txt"); esfile<<"Nummber of rows: "<SetInput( 0, const_cast( surface ) ); } void mitk::CreateDistanceImageFromSurfaceFilter::SetInput( unsigned int idx, const mitk::Surface* surface ) { if ( this->GetInput(idx) != surface ) { this->SetNthInput( idx, const_cast( surface ) ); this->Modified(); } } const mitk::Surface* mitk::CreateDistanceImageFromSurfaceFilter::GetInput() { if (this->GetNumberOfIndexedInputs() < 1) return NULL; return static_cast(this->ProcessObject::GetInput(0)); } const mitk::Surface* mitk::CreateDistanceImageFromSurfaceFilter::GetInput( unsigned int idx) { if (this->GetNumberOfIndexedInputs() < 1) return NULL; return static_cast(this->ProcessObject::GetInput(idx)); } void mitk::CreateDistanceImageFromSurfaceFilter::RemoveInputs(mitk::Surface* input) { DataObjectPointerArraySizeType nb = this->GetNumberOfIndexedInputs(); for(DataObjectPointerArraySizeType i = 0; i < nb; i++) { if( this->GetInput(i) == input ) { this->RemoveInput(i); return; } } } void mitk::CreateDistanceImageFromSurfaceFilter::Reset() { for (unsigned int i = 0; i < this->GetNumberOfIndexedInputs(); i++) { this->PopBackInput(); } this->SetNumberOfIndexedInputs(0); this->SetNumberOfIndexedOutputs(1); mitk::Image::Pointer output = mitk::Image::New(); this->SetNthOutput(0, output.GetPointer()); } void mitk::CreateDistanceImageFromSurfaceFilter::SetUseProgressBar(bool status) { this->m_UseProgressBar = status; } void mitk::CreateDistanceImageFromSurfaceFilter::SetProgressStepSize(unsigned int stepSize) { this->m_ProgressStepSize = stepSize; }