Attenuation

VTKEx/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 simple question about this example contact us at VTKExProject If your question is more complex and may require extended discussion, please use the VTK Discourse Forum

Code¶

Attenuation.cxx

#include <vtkImageActor.h>
#include <vtkImageCast.h>
#include <vtkImageCast.h>
#include <vtkImageGaussianSmooth.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 <vtkInteractorStyleImage.h>
#include <vtkNamedColors.h>
#include <vtkRenderer.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkSampleFunction.h>
#include <vtkSmartPointer.h>
#include <vtkSphere.h>

int main (int argc, char *argv[])
{

  // Verify input arguments
  if ( argc != 2 )
  {
    std::cout << "Usage: " << argv[0]
              << " Filename" << std::endl;
    return EXIT_FAILURE;
  }

  // Read the image
  vtkSmartPointer<vtkImageReader2Factory> readerFactory =
    vtkSmartPointer<vtkImageReader2Factory>::New();
  vtkSmartPointer<vtkImageReader2> reader;
  reader.TakeReference(
    readerFactory->CreateImageReader2(argv[1]));
  reader->SetFileName(argv[1]);

  vtkSmartPointer<vtkImageCast> cast =
    vtkSmartPointer<vtkImageCast>::New();
  cast->SetInputConnection(reader->GetOutputPort());
  cast->SetOutputScalarTypeToDouble();

// get rid of discrete scalars);
  vtkSmartPointer<vtkImageGaussianSmooth> smooth =
    vtkSmartPointer<vtkImageGaussianSmooth>::New();
  smooth->SetInputConnection(cast->GetOutputPort());
  smooth->SetStandardDeviations(0.8, 0.8, 0);

  vtkSmartPointer<vtkSphere> m1 =
    vtkSmartPointer<vtkSphere>::New();
  m1->SetCenter(310, 130, 0);
  m1->SetRadius(0);

  vtkSmartPointer<vtkSampleFunction> m2 =
    vtkSmartPointer<vtkSampleFunction>::New();
  m2->SetImplicitFunction(m1);
  m2->SetModelBounds(0, 264, 0, 264, 0, 1);
  m2->SetSampleDimensions(264, 264, 1);

  vtkSmartPointer<vtkImageShiftScale> m3 =
    vtkSmartPointer<vtkImageShiftScale>::New();
  m3->SetInputConnection(m2->GetOutputPort());
  m3->SetScale(0.000095);

  vtkSmartPointer<vtkImageMathematics> div =
    vtkSmartPointer<vtkImageMathematics>::New();
  div->SetInputConnection(0, smooth->GetOutputPort());
  div->SetInputConnection(1, m3->GetOutputPort());
  div->SetOperationToMultiply();

  // Create actors
  vtkSmartPointer<vtkNamedColors> colors =
    vtkSmartPointer<vtkNamedColors>::New();

  double colorWindow = 256.0;
  double colorLevel = 127.5;
  vtkSmartPointer<vtkImageActor> originalActor =
    vtkSmartPointer<vtkImageActor>::New();
  originalActor->GetMapper()->SetInputConnection(cast->GetOutputPort());
  originalActor->GetProperty()->SetColorWindow(colorWindow);
  originalActor->GetProperty()->SetColorLevel(colorLevel);

  vtkSmartPointer<vtkImageActor> filteredActor =
    vtkSmartPointer<vtkImageActor>::New();
  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
  vtkSmartPointer<vtkRenderer> originalRenderer =
    vtkSmartPointer<vtkRenderer>::New();
  originalRenderer->SetViewport(originalViewport);
  originalRenderer->AddActor(originalActor);
  originalRenderer->ResetCamera();
  originalRenderer->SetBackground(colors->GetColor3d("SlateGray").GetData());

  vtkSmartPointer<vtkRenderer> filteredRenderer =
    vtkSmartPointer<vtkRenderer>::New();
  filteredRenderer->SetViewport(filteredViewport);
  filteredRenderer->AddActor(filteredActor);
  filteredRenderer->ResetCamera();
  filteredRenderer->SetBackground(colors->GetColor3d("LightSlateGray").GetData());

  vtkSmartPointer<vtkRenderWindow> renderWindow =
    vtkSmartPointer<vtkRenderWindow>::New();
  renderWindow->SetSize(600, 300);
  renderWindow->AddRenderer(originalRenderer);
  renderWindow->AddRenderer(filteredRenderer);

  vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor =
    vtkSmartPointer<vtkRenderWindowInteractor>::New();
  vtkSmartPointer<vtkInteractorStyleImage> style =
    vtkSmartPointer<vtkInteractorStyleImage>::New();

  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 
  vtkvtkCommonColor
  vtkvtkCommonCore
  vtkvtkCommonDataModel
  vtkvtkIOImage
  vtkvtkImagingCore
  vtkvtkImagingGeneral
  vtkvtkImagingHybrid
  vtkvtkImagingMath
  vtkvtkInteractionStyle
  vtkvtkRenderingContextOpenGL2
  vtkvtkRenderingCore
  vtkvtkRenderingFreeType
  vtkvtkRenderingGL2PSOpenGL2
  vtkvtkRenderingOpenGL2 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.