IsoSubsample
VTKExamples/Cxx/ImageProcessing/IsoSubsample
Description¶
An artifact called aliasing occurs when sub-sampling and is often associated with stair-stepping edges. Sampling theory proves that discrete sampled signals with spacing S, completely describe continuous functions composed of frequencies less than S/2. When a signal is sub-sampled, its capacity to hold high frequency information is reduced. However, the high frequency energy does not disappear. It wraps around the frequency spectrum appearing as a low frequency alias artifact. The solution, which eliminates this artifact, is to low-pass filter before sub-sampling.
Low-pass smoothing reduces the high frequency range of an image that would cause aliasing. The same aliasing phenomena occurs when acquiring data. If a signal from an analog source contains high frequencies, saving the analog data in a discrete form requires sub-sampling that will introduce alias artifacts. For this reason, it is common practice to acquire data at high resolutions,then smooth and subsample to reduce the image to a manageable size.
This example demonstrates aliasing that occurs when a high-frequency signal is sub-sampled. High frequencies appear as low frequency artifacts. The left image is an isosurface of a skull after sub-sampling. The right image used a low-pass filter before sub-sampling to reduce aliasing.
Note
This example uses the FullHead.mhd, FullHead.raw.gz dataset.
Info
See this figure in Chapter 10 the VTK Textbook.
Other Languages
See (Python)
Code¶
IsoSubsample.cxx
#include <vtkActor.h> #include <vtkCamera.h> #include <vtkImageGaussianSmooth.h> #include <vtkImageMarchingCubes.h> #include <vtkImageReader2.h> #include <vtkImageReader2Factory.h> #include <vtkImageShrink3D.h> #include <vtkNamedColors.h> #include <vtkPolyDataMapper.h> #include <vtkProperty.h> #include <vtkRenderer.h> #include <vtkRenderWindow.h> #include <vtkRenderWindowInteractor.h> #include <vtkSmartPointer.h> #include <array> int main (int argc, char *argv[]) { // Verify input arguments if ( argc != 2 ) { std::cout << "Usage: " << argv[0] << " Filename" << std::endl; return EXIT_FAILURE; } vtkSmartPointer<vtkNamedColors> colors = vtkSmartPointer<vtkNamedColors>::New(); std::array<unsigned char , 4> actorColor{{235, 235, 235, 255}}; colors->SetColor("ActorColor", actorColor.data()); // Read the image vtkSmartPointer<vtkImageReader2Factory> readerFactory = vtkSmartPointer<vtkImageReader2Factory>::New(); vtkSmartPointer<vtkImageReader2> reader = readerFactory->CreateImageReader2(argv[1]); reader->SetFileName(argv[1]); reader->Update(); // Smoothed pipeline vtkSmartPointer<vtkImageGaussianSmooth> smooth = vtkSmartPointer<vtkImageGaussianSmooth>::New(); smooth->SetDimensionality(3); smooth->SetInputConnection(reader->GetOutputPort()); smooth->SetStandardDeviations(1.75, 1.75, 0.0); smooth->SetRadiusFactor(2); vtkSmartPointer<vtkImageShrink3D> subsampleSmoothed = vtkSmartPointer<vtkImageShrink3D>::New(); subsampleSmoothed->SetInputConnection(smooth->GetOutputPort()); subsampleSmoothed->SetShrinkFactors(4, 4, 1); vtkSmartPointer<vtkImageMarchingCubes> isoSmoothed = vtkSmartPointer<vtkImageMarchingCubes>::New(); isoSmoothed->SetInputConnection(smooth->GetOutputPort()); isoSmoothed->SetValue(0, 1150); vtkSmartPointer<vtkPolyDataMapper> isoSmoothedMapper = vtkSmartPointer<vtkPolyDataMapper>::New(); isoSmoothedMapper->SetInputConnection(isoSmoothed->GetOutputPort()); isoSmoothedMapper->ScalarVisibilityOff(); vtkSmartPointer<vtkActor> isoSmoothedActor = vtkSmartPointer<vtkActor>::New(); isoSmoothedActor->SetMapper(isoSmoothedMapper); isoSmoothedActor->GetProperty()->SetColor(colors->GetColor3d("ActorColor").GetData()); // Unsmoothed pipeline // Sub sample the data vtkSmartPointer<vtkImageShrink3D> subsample = vtkSmartPointer<vtkImageShrink3D>::New(); subsample->SetInputConnection(reader->GetOutputPort()); subsample->SetShrinkFactors(4, 4, 1); vtkSmartPointer<vtkImageMarchingCubes> iso = vtkSmartPointer<vtkImageMarchingCubes>::New(); iso->SetInputConnection(subsample->GetOutputPort()); iso->SetValue(0, 1150); vtkSmartPointer<vtkPolyDataMapper> isoMapper = vtkSmartPointer<vtkPolyDataMapper>::New(); isoMapper->SetInputConnection(iso->GetOutputPort()); isoMapper->ScalarVisibilityOff(); vtkSmartPointer<vtkActor> isoActor = vtkSmartPointer<vtkActor>::New(); isoActor->SetMapper(isoMapper); isoActor->GetProperty()->SetColor(colors->GetColor3d("ActorColor").GetData()); // Rendering Pipeline // Setup render window, renderer, and interactor double leftViewport[4] = {0.0, 0.0, 0.5, 1.0}; double rightViewport[4] = {0.5, 0.0, 1.0, 1.0}; vtkSmartPointer<vtkRenderer> rendererLeft = vtkSmartPointer<vtkRenderer>::New(); rendererLeft->SetViewport(leftViewport); vtkSmartPointer<vtkRenderer> rendererRight = vtkSmartPointer<vtkRenderer>::New(); rendererRight->SetViewport(rightViewport); vtkSmartPointer<vtkRenderWindow> renderWindow = vtkSmartPointer<vtkRenderWindow>::New(); renderWindow->AddRenderer(rendererLeft); renderWindow->AddRenderer(rendererRight); vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor = vtkSmartPointer<vtkRenderWindowInteractor>::New(); renderWindowInteractor->SetRenderWindow(renderWindow); rendererLeft->AddActor(isoActor); rendererRight->AddActor(isoSmoothedActor); rendererLeft->GetActiveCamera()->SetFocalPoint(0.0, 0.0, 0.0); rendererLeft->GetActiveCamera()->SetPosition(0.0, -1.0, 0.0); rendererLeft->GetActiveCamera()->SetViewUp(0.0, 0.0, -1.0); rendererLeft->ResetCamera(); rendererLeft->GetActiveCamera()->Azimuth(-20.0); rendererLeft->GetActiveCamera()->Elevation(20.0); rendererLeft->ResetCameraClippingRange(); rendererLeft->SetBackground(colors->GetColor3d("SlateGray").GetData()); rendererRight->SetBackground(colors->GetColor3d("LightSlateGray").GetData()); rendererRight->SetActiveCamera(rendererLeft->GetActiveCamera()); renderWindow->SetSize(640, 480); renderWindow->Render(); renderWindowInteractor->Start(); return EXIT_SUCCESS; }
CMakeLists.txt¶
cmake_minimum_required(VERSION 3.3 FATAL_ERROR) project(IsoSubsample) find_package(VTK COMPONENTS vtkCommonColor vtkCommonCore vtkFiltersGeneral vtkIOImage vtkImagingCore vtkImagingGeneral vtkInteractionStyle vtkRenderingCore vtkRenderingFreeType vtkRenderingOpenGL2 QUIET) if (NOT VTK_FOUND) message("Skipping IsoSubsample: ${VTK_NOT_FOUND_MESSAGE}") return () endif() message (STATUS "VTK_VERSION: ${VTK_VERSION}") if (VTK_VERSION VERSION_LESS "8.90.0") # old system include(${VTK_USE_FILE}) add_executable(IsoSubsample MACOSX_BUNDLE IsoSubsample.cxx ) target_link_libraries(IsoSubsample PRIVATE ${VTK_LIBRARIES}) else () # include all components add_executable(IsoSubsample MACOSX_BUNDLE IsoSubsample.cxx ) target_link_libraries(IsoSubsample PRIVATE ${VTK_LIBRARIES}) # vtk_module_autoinit is needed vtk_module_autoinit( TARGETS IsoSubsample MODULES ${VTK_LIBRARIES} ) endif ()
Download and Build IsoSubsample¶
Click here to download IsoSubsample and its CMakeLists.txt file. Once the tarball IsoSubsample.tar has been downloaded and extracted,
cd IsoSubsample/build
If VTK is installed:
cmake ..
If VTK is not installed but compiled on your system, you will need to specify the path to your VTK build:
cmake -DVTK_DIR:PATH=/home/me/vtk_build ..
Build the project:
make
and run it:
./IsoSubsample
WINDOWS USERS
Be sure to add the VTK bin directory to your path. This will resolve the VTK dll's at run time.