Attenuation

VTKExamples/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)

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 =
    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 
  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.