Landmark Registration

This example demonstrates the use of point based registration. This form of registration is often used to initialize an intensity based registration that refines the results of the point base method, hence the “initializer” in the class name. The example uses a 2D rigid transformation, though the LandmarkBasedTransformInitializerFilter class supports other transformation types including VersorRigid3DTransform, AffineTransform and BSplineTransform.

If you are not familiar with the SimpleITK registration framework we recommend that you read the registration overview before continuing with the example.

Overview

Code

C++C#JavaPythonR

#include <SimpleITK.h>
#include <iostream>
#include <vector>

namespace sitk = itk::simple;

int
main(int argc, char * argv[])
{
  using sitk::operator<<;

  // Black image with a small white square in it.
  sitk::Image fixedImage(100, 100, sitk::sitkUInt8);
  // Paste a white square (9x9 pixels with value 200) at position [11, 11]
  sitk::PasteImageFilter pasteFilter;
  pasteFilter.SetSourceSize({ 9, 9 });
  pasteFilter.SetSourceIndex({ 0, 0 });
  pasteFilter.SetDestinationIndex({ 11, 11 });
  fixedImage = pasteFilter.Execute(fixedImage, 200);

  // Black image with a small grey square at a different location.
  sitk::Image movingImage(100, 100, sitk::sitkUInt8);
  // Paste a grey square (9x9 pixels with value 69) at position [51, 51]
  pasteFilter.SetDestinationIndex({ 51, 51 });
  movingImage = pasteFilter.Execute(movingImage, 69);

  // Landmarks are 3 corners of the squares.
  // 3 (X, Y) pairs are flattened into 1-d lists.
  std::vector<double> fixedLandmarks = { 10, 10, 20, 10, 20, 20 };
  std::vector<double> movingLandmarks = { 50, 50, 60, 50, 60, 60 };

  // Set up the LandmarkBasedTransformInitializerFilter.
  sitk::LandmarkBasedTransformInitializerFilter landmarkInitializer;

  landmarkInitializer.SetFixedLandmarks(fixedLandmarks);
  landmarkInitializer.SetMovingLandmarks(movingLandmarks);

  sitk::Transform transform = sitk::Euler2DTransform();

  // Compute the transform.
  sitk::Transform outputTransform = landmarkInitializer.Execute(transform);

  std::cout << outputTransform.ToString() << std::endl;

  // Resample the transformed moving image onto the fixed image.
  sitk::Image outputImage = sitk::Resample(movingImage, fixedImage, outputTransform, sitk::sitkLinear, 150);

  // Write the resampled image.
  sitk::WriteImage(outputImage, "landmark_example.png");

  // Write the transform.
  std::string outName;
  if (argc > 1)
  {
    outName = argv[1];
  }
  else
  {
    outName = "landmark_transform.tfm";
  }

  sitk::WriteTransform(outputTransform, outName);

  return 0;
}