void WorkbenchUtils::addPaddingItk(itk::Image <PixelType, ImageDimension> *itkImage, Axis axis, bool append,
int numberOfSlices, float pixelValue, Image::Pointer outImage) {
// pixel type is templated. The input field for the value is set to float, so the user might enter some invalid values for the image type at hand.
// since all primitive built-in types have well defined casting behaviour between each other, we'll just do a typecast. we will clip the entered
// value at PixelTypes min/max to prevent an overflow. The possible loss of precision is ignored.
float lower = itk::NumericTraits<PixelType>::min();
float upper = itk::NumericTraits<PixelType>::max();
float clippedPixelValue = std::max(lower, std::min(pixelValue, upper));
PixelType paddingPixelValue = (PixelType) clippedPixelValue;
typedef itk::Image <PixelType, ImageDimension> ImageType;
// gather all data
typename ImageType::SizeType lowerBound;
typename ImageType::SizeType upperBound;
lowerBound.Fill(0);
upperBound.Fill(0);
unsigned int itkAxis = convertToItkAxis(axis);
if (append) {
upperBound[itkAxis] = numberOfSlices;
} else {
lowerBound[itkAxis] = numberOfSlices;
}
// setup the filter
typedef itk::ConstantPadImageFilter <ImageType, ImageType> PadFilterType;
typename PadFilterType::Pointer padFilter = PadFilterType::New();
padFilter->SetInput(itkImage);
padFilter->SetConstant(paddingPixelValue);
padFilter->SetPadLowerBound(lowerBound);
padFilter->SetPadUpperBound(upperBound);
padFilter->UpdateLargestPossibleRegion();
// Update the origin, since padding creates negative index that is lost when returned to MITK
typename ImageType::Pointer paddedImage = padFilter->GetOutput();
typename ImageType::RegionType paddedImageRegion = paddedImage->GetLargestPossibleRegion();
typename ImageType::PointType origin;
paddedImage->TransformIndexToPhysicalPoint(paddedImageRegion.GetIndex(), origin);
paddedImage->SetOrigin(origin);
// get the results and cast them back to mitk. return via out parameter.
outImage->InitializeByItk(paddedImage.GetPointer());
CastToMitkImage(paddedImage, outImage);
}
void mitk::ImageToContourFilter::Itk2DContourExtraction(const itk::Image<TPixel, VImageDimension> *sliceImage)
{
typedef itk::Image<TPixel, VImageDimension> ImageType;
typedef itk::ContourExtractor2DImageFilter<ImageType> ContourExtractor;
typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
typename PadFilterType::Pointer padFilter = PadFilterType::New();
typename ImageType::SizeType lowerExtendRegion;
lowerExtendRegion[0] = 1;
lowerExtendRegion[1] = 1;
typename ImageType::SizeType upperExtendRegion;
upperExtendRegion[0] = 1;
upperExtendRegion[1] = 1;
/*
* We need to pad here, since the ITK contour extractor fails if the
* segmentation touches more than one image edge.
* By padding the image for one row at each edge we overcome this issue
*/
padFilter->SetInput(sliceImage);
padFilter->SetConstant(0);
padFilter->SetPadLowerBound(lowerExtendRegion);
padFilter->SetPadUpperBound(upperExtendRegion);
typename ContourExtractor::Pointer contourExtractor = ContourExtractor::New();
contourExtractor->SetInput(padFilter->GetOutput());
contourExtractor->SetContourValue(0.5);
contourExtractor->Update();
unsigned int foundPaths = contourExtractor->GetNumberOfOutputs();
vtkSmartPointer<vtkPolyData> contourSurface = vtkSmartPointer<vtkPolyData>::New();
vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> polygons = vtkSmartPointer<vtkCellArray>::New();
unsigned int pointId(0);
for (unsigned int i = 0; i < foundPaths; i++)
{
const ContourPath *currentPath = contourExtractor->GetOutput(i)->GetVertexList();
vtkSmartPointer<vtkPolygon> polygon = vtkSmartPointer<vtkPolygon>::New();
polygon->GetPointIds()->SetNumberOfIds(currentPath->Size());
Point3D currentPoint;
Point3D currentWorldPoint;
for (unsigned int j = 0; j < currentPath->Size(); j++)
{
currentPoint[0] = currentPath->ElementAt(j)[0];
currentPoint[1] = currentPath->ElementAt(j)[1];
currentPoint[2] = 0;
m_SliceGeometry->IndexToWorld(currentPoint, currentWorldPoint);
points->InsertPoint(pointId, currentWorldPoint[0], currentWorldPoint[1], currentWorldPoint[2]);
polygon->GetPointIds()->SetId(j, pointId);
pointId++;
} // for2
polygons->InsertNextCell(polygon);
} // for1
contourSurface->SetPoints(points);
contourSurface->SetPolys(polygons);
contourSurface->BuildLinks();
Surface::Pointer finalSurface = this->GetOutput();
finalSurface->SetVtkPolyData(contourSurface);
}
void mitk::ImageToContourModelFilter::Itk2DContourExtraction (const itk::Image<TPixel, VImageDimension>* sliceImage)
{
typedef itk::Image<TPixel, VImageDimension> ImageType;
typedef itk::ContourExtractor2DImageFilter<ImageType> ContourExtractor;
typedef itk::PolyLineParametricPath<2> PolyLineParametricPath2D;
typedef PolyLineParametricPath2D::VertexListType ContourPath;
typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
typename PadFilterType::Pointer padFilter = PadFilterType::New();
typename ImageType::SizeType lowerExtendRegion;
lowerExtendRegion[0] = 1;
lowerExtendRegion[1] = 1;
typename ImageType::SizeType upperExtendRegion;
upperExtendRegion[0] = 1;
upperExtendRegion[1] = 1;
/*
* We need to pad here, since the ITK contour extractor fails if the
* segmentation touches more than one image edge.
* By padding the image for one row at each edge we overcome this issue
*/
padFilter->SetInput(sliceImage);
padFilter->SetConstant(0);
padFilter->SetPadLowerBound(lowerExtendRegion);
padFilter->SetPadUpperBound(upperExtendRegion);
typename ContourExtractor::Pointer contourExtractor = ContourExtractor::New();
contourExtractor->SetInput(padFilter->GetOutput());
contourExtractor->SetContourValue(m_ContourValue);
contourExtractor->Update();
unsigned int foundPaths = contourExtractor->GetNumberOfOutputs();
this->SetNumberOfIndexedOutputs(foundPaths);
for (unsigned int i = 0; i < foundPaths; i++)
{
const ContourPath* currentPath = contourExtractor->GetOutput(i)->GetVertexList();
mitk::Point3D currentPoint;
mitk::Point3D currentWorldPoint;
mitk::ContourModel::Pointer contour = this->GetOutput(i);
if (contour.IsNull())
{
contour = mitk::ContourModel::New();
}
if (contour.IsNull())
contour = mitk::ContourModel::New();
for (unsigned int j = 0; j < currentPath->Size(); j++)
{
currentPoint[0] = currentPath->ElementAt(j)[0];
currentPoint[1] = currentPath->ElementAt(j)[1];
currentPoint[2] = 0;
m_SliceGeometry->IndexToWorld(currentPoint, currentWorldPoint);
contour->AddVertex(currentWorldPoint);
}//for2
contour->Close();
}//for1
}
