Elastix/elx.cxx

// This one header will include all SimpleITK filters and external
// objects.
#include <SimpleITK.h>
#include <iostream>
#include <stdlib.h>
 
namespace sitk = itk::simple;
 
int
main(int argc, char * argv[])
{
 
  if (argc < 5)
  {
    std::cerr << "Usage: " << argv[0]
              << " <fixedImage> <movingImage> <parameterFile> <outputImage> <outputParameterFile> \n";
    return 1;
  }
 
  // Instantiate SimpleElastix
  sitk::ElastixImageFilter elastixImageFilter;
 
  // Read input
  sitk::ImageFileReader reader;
  reader.SetFileName(std::string(argv[1]));
  elastixImageFilter.SetFixedImage(reader.Execute());
  reader.SetFileName(std::string(argv[2]));
  elastixImageFilter.SetMovingImage(reader.Execute());
  elastixImageFilter.SetParameterMap(sitk::ReadParameterFile(std::string(argv[3])));
  elastixImageFilter.LogToConsoleOn();
 
  // Run registration
  elastixImageFilter.Execute();
 
  // Write result image
  sitk::ImageFileWriter writer;
  writer.SetFileName(std::string(argv[4]));
  writer.Execute(elastixImageFilter.GetResultImage());
 
  // Write parameter file. This test executable only supports one parameter map and one transform parameter map.
  sitk::WriteParameterFile(elastixImageFilter.GetTransformParameterMaps()[0], std::string(argv[5]));
  return 0;
}