Attenuation
vtk-examples/Cxx/ImageProcessing/Attenuation
Description¶
This MRI image illustrates attenuation that can occur due to sensor position. The artifact is removed by dividing by the attenuation profile determined manually. This histograms shows how the artifact hides information in the form of scalar value clusters.
Info
See this figure in Chapter 10 the VTK Textbook.
Other languages
See (Python)
Question
If you have a question about this example, please use the VTK Discourse Forum
Code¶
Attenuation.cxx
#include <vtkImageActor.h>
#include <vtkImageCast.h>
#include <vtkImageGaussianSmooth.h>
#include <vtkImageMapper3D.h>
#include <vtkImageMathematics.h>
#include <vtkImageProperty.h>
#include <vtkImageReader2.h>
#include <vtkImageReader2Factory.h>
#include <vtkImageShiftScale.h>
#include <vtkInteractorStyleImage.h>
#include <vtkNamedColors.h>
#include <vtkNew.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkRenderer.h>
#include <vtkSampleFunction.h>
#include <vtkSphere.h>
int main(int argc, char* argv[])
{
// Verify input arguments
if (argc != 2)
{
std::cout << "Usage: " << argv[0] << " Filename e.g. AttenuationArtifact.pg"
<< std::endl;
return EXIT_FAILURE;
}
// Read the image
vtkNew<vtkImageReader2Factory> readerFactory;
vtkSmartPointer<vtkImageReader2> reader;
reader.TakeReference(readerFactory->CreateImageReader2(argv[1]));
reader->SetFileName(argv[1]);
vtkNew<vtkImageCast> cast;
cast->SetInputConnection(reader->GetOutputPort());
cast->SetOutputScalarTypeToDouble();
// get rid of discrete scalars);
vtkNew<vtkImageGaussianSmooth> smooth;
smooth->SetInputConnection(cast->GetOutputPort());
smooth->SetStandardDeviations(0.8, 0.8, 0);
vtkNew<vtkSphere> m1;
m1->SetCenter(310, 130, 0);
m1->SetRadius(0);
vtkNew<vtkSampleFunction> m2;
m2->SetImplicitFunction(m1);
m2->SetModelBounds(0, 264, 0, 264, 0, 1);
m2->SetSampleDimensions(264, 264, 1);
vtkNew<vtkImageShiftScale> m3;
m3->SetInputConnection(m2->GetOutputPort());
m3->SetScale(0.000095);
vtkNew<vtkImageMathematics> div;
div->SetInputConnection(0, smooth->GetOutputPort());
div->SetInputConnection(1, m3->GetOutputPort());
div->SetOperationToMultiply();
// Create actors
vtkNew<vtkNamedColors> colors;
double colorWindow = 256.0;
double colorLevel = 127.5;
vtkNew<vtkImageActor> originalActor;
originalActor->GetMapper()->SetInputConnection(cast->GetOutputPort());
originalActor->GetProperty()->SetColorWindow(colorWindow);
originalActor->GetProperty()->SetColorLevel(colorLevel);
vtkNew<vtkImageActor> filteredActor;
filteredActor->GetMapper()->SetInputConnection(div->GetOutputPort());
// Define viewport ranges
// (xmin, ymin, xmax, ymax)
double originalViewport[4] = {0.0, 0.0, 0.5, 1.0};
double filteredViewport[4] = {0.5, 0.0, 1.0, 1.0};
// Setup renderers
vtkNew<vtkRenderer> originalRenderer;
originalRenderer->SetViewport(originalViewport);
originalRenderer->AddActor(originalActor);
originalRenderer->ResetCamera();
originalRenderer->SetBackground(colors->GetColor3d("SlateGray").GetData());
vtkNew<vtkRenderer> filteredRenderer;
filteredRenderer->SetViewport(filteredViewport);
filteredRenderer->AddActor(filteredActor);
filteredRenderer->ResetCamera();
filteredRenderer->SetBackground(
colors->GetColor3d("LightSlateGray").GetData());
vtkNew<vtkRenderWindow> renderWindow;
renderWindow->SetSize(600, 300);
renderWindow->AddRenderer(originalRenderer);
renderWindow->AddRenderer(filteredRenderer);
renderWindow->SetWindowName("Attenuation");
vtkNew<vtkRenderWindowInteractor> renderWindowInteractor;
vtkNew<vtkInteractorStyleImage> style;
renderWindowInteractor->SetInteractorStyle(style);
renderWindowInteractor->SetRenderWindow(renderWindow);
renderWindow->Render();
renderWindowInteractor->Initialize();
renderWindowInteractor->Start();
return EXIT_SUCCESS;
}
CMakeLists.txt¶
cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
project(Attenuation)
find_package(VTK COMPONENTS
vtkCommonColor
vtkCommonCore
vtkCommonDataModel
vtkIOImage
vtkImagingCore
vtkImagingGeneral
vtkImagingHybrid
vtkImagingMath
vtkInteractionStyle
vtkRenderingContextOpenGL2
vtkRenderingCore
vtkRenderingFreeType
vtkRenderingGL2PSOpenGL2
vtkRenderingOpenGL2
QUIET
)
if (NOT VTK_FOUND)
message("Skipping Attenuation: ${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(Attenuation MACOSX_BUNDLE Attenuation.cxx )
target_link_libraries(Attenuation PRIVATE ${VTK_LIBRARIES})
else ()
# include all components
add_executable(Attenuation MACOSX_BUNDLE Attenuation.cxx )
target_link_libraries(Attenuation PRIVATE ${VTK_LIBRARIES})
# vtk_module_autoinit is needed
vtk_module_autoinit(
TARGETS Attenuation
MODULES ${VTK_LIBRARIES}
)
endif ()
Download and Build Attenuation¶
Click here to download Attenuation and its CMakeLists.txt file. Once the tarball Attenuation.tar has been downloaded and extracted,
cd Attenuation/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:
./Attenuation
WINDOWS USERS
Be sure to add the VTK bin directory to your path. This will resolve the VTK dll's at run time.