Difference between revisions of "ITK/Examples/SpectralAnalysis/CrossCorrelationInFourierDomain"

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(Created page with "==VnlFFTRealToComplexConjugateImageFilter.cxx== <source lang="cpp"> #include "itkImage.h" #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #include "itkVnlFFTRealT...")
 
 
(9 intermediate revisions by 3 users not shown)
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==VnlFFTRealToComplexConjugateImageFilter.cxx==
In ITKv4, ''VnlFFTRealToComplexConjugateImageFilter'' was renamed V''nlForwardFFTImageFilter'' and ''VnlFFTComplexConjugateToRealImageFilter'' was renamed ''VnlInverseFFTImageFilter''.
==CrossCorrelationInFourierDomain.cxx==
<source lang="cpp">
<source lang="cpp">
#include "itkImage.h"
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImageFileWriter.h"
#if ITK_VERSION_MAJOR < 4
#include "itkVnlFFTRealToComplexConjugateImageFilter.h"
#include "itkVnlFFTRealToComplexConjugateImageFilter.h"
#include "itkVnlFFTComplexConjugateToRealImageFilter.h"
#include "itkVnlFFTComplexConjugateToRealImageFilter.h"
#else
#include "itkVnlForwardFFTImageFilter.h"
#include "itkVnlInverseFFTImageFilter.h"
#endif
#include "itkComplexToRealImageFilter.h"
#include "itkComplexToImaginaryImageFilter.h"
#include "itkMultiplyImageFilter.h"
#include "itkMultiplyImageFilter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkFFTShiftImageFilter.h"
#include "itkMinimumMaximumImageCalculator.h"


#if ITK_VERSION_MAJOR < 4
#include "itkMultiplyByConstantImageFilter.h"
#include "itkRealAndImaginaryToComplexImageFilter.h"
#else
#include "itkComposeImageFilter.h"
#endif


int main( int argc, char * argv [] )
int main(int argc, char*argv[])
{
{
   if( argc < 4 )
  const    unsigned int    Dimension = 2;
  typedef  float                                  PixelType;
  typedef itk::Image< PixelType, Dimension >      FloatImageType;
  typedef itk::Image< unsigned char, Dimension >  UnsignedCharImageType;
 
   if( argc < 3 )
     {
     {
     std::cerr << "Usage: " << argv[0] << " inputScalarImage  inputMaskImage";
    std::cerr << "Missing Parameters " << std::endl;
     std::cerr << " outputFilteredImage" << std::endl;
     std::cerr << "Usage: " << argv[0];
     std::cerr << " FixedImage MovingImage"<< std::endl;;
    return EXIT_FAILURE;
     }
     }
  std::string fixedImageFilename = argv[1];
  std::string movingImageFilename = argv[2];


   typedef float InputPixelType;
  // Read the input images
   const unsigned int Dimension = 2;
   typedef itk::ImageFileReader< FloatImageType  > ImageReaderType;
  ImageReaderType::Pointer fixedImageReader  = ImageReaderType::New();
  fixedImageReader->SetFileName( fixedImageFilename );
  fixedImageReader->Update();
    
  ImageReaderType::Pointer movingImageReader = ImageReaderType::New();
  movingImageReader->SetFileName( movingImageFilename );
  movingImageReader->Update();


   typedef itk::Image< InputPixelType, Dimension > InputImageType;
  // Shift the input images
   typedef itk::FFTShiftImageFilter< FloatImageType, FloatImageType > FFTShiftFilterType;
  FFTShiftFilterType::Pointer fixedFFTShiftFilter = FFTShiftFilterType::New();
  fixedFFTShiftFilter->SetInput(fixedImageReader->GetOutput());
  fixedFFTShiftFilter->Update();


   typedef itk::ImageFileReader< InputImageType >   InputReaderType;
  FFTShiftFilterType::Pointer movingFFTShiftFilter = FFTShiftFilterType::New();
 
  movingFFTShiftFilter->SetInput(movingImageReader->GetOutput());
   InputReaderType::Pointer inputReader1 = InputReaderType::New();
  movingFFTShiftFilter->Update();
   InputReaderType::Pointer inputReader2 = InputReaderType::New();
 
 
  // Compute the FFT of the input
   inputReader1->SetFileName( argv[1] );
#if ITK_VERSION_MAJOR < 4
   inputReader2->SetFileName( argv[2] );
  typedef itk::VnlFFTRealToComplexConjugateImageFilter< FloatImageType >  FFTFilterType;
#else
   typedef itk::VnlForwardFFTImageFilter< FloatImageType > FFTFilterType;
#endif
   FFTFilterType::Pointer fixedFFTFilter = FFTFilterType::New();
   fixedFFTFilter->SetInput( fixedFFTShiftFilter->GetOutput() );
  fixedFFTFilter->Update();
 
  FFTFilterType::Pointer movingFFTFilter = FFTFilterType::New();
   movingFFTFilter->SetInput( movingFFTShiftFilter->GetOutput() );
    
  typedef FFTFilterType::OutputImageType    SpectralImageType;


   typedef itk::VnlFFTRealToComplexConjugateImageFilter<
  // Take the conjugate of the fftFilterMoving
                                  InputPixelType, Dimension > FFTFilterType;
  // Extract the real part
   typedef itk::ComplexToRealImageFilter<SpectralImageType, FloatImageType> RealFilterType;
  RealFilterType::Pointer realFilter = RealFilterType::New();
  realFilter->SetInput(movingFFTFilter->GetOutput());


   FFTFilterType::Pointer fftFilter1 = FFTFilterType::New();
   // Extract the imaginary part
   FFTFilterType::Pointer fftFilter2 = FFTFilterType::New();
  typedef itk::ComplexToImaginaryImageFilter<SpectralImageType, FloatImageType> ImaginaryFilterType;
  ImaginaryFilterType::Pointer imaginaryFilter = ImaginaryFilterType::New();
   imaginaryFilter->SetInput(movingFFTFilter->GetOutput());


   fftFilter1->SetInput( inputReader1->GetOutput() );
   // Flip the sign of the imaginary and combine with the real part again
   fftFilter2->SetInput( inputReader2->GetOutput() );
#if ITK_VERSION_MAJOR < 4
  typedef itk::MultiplyByConstantImageFilter<FloatImageType,PixelType,FloatImageType> MultiplyConstantFilterType;
#else
   typedef itk::MultiplyImageFilter<FloatImageType,FloatImageType,FloatImageType> MultiplyConstantFilterType;
#endif


   typedef FFTFilterType::OutputImageType    SpectralImageType;
  MultiplyConstantFilterType::Pointer flipSignFilter = MultiplyConstantFilterType::New();
#if ITK_VERSION_MAJOR < 4
  flipSignFilter->SetConstant(-1);
#else
  flipSignFilter->SetConstant2(-1);
#endif
  flipSignFilter->SetInput(imaginaryFilter->GetOutput());
#if ITK_VERSION_MAJOR < 4
   typedef itk::RealAndImaginaryToComplexImageFilter<FloatImageType> RealImageToComplexFilterType;
#else
  typedef itk::ComposeImageFilter<FloatImageType, SpectralImageType> RealImageToComplexFilterType;
#endif
  RealImageToComplexFilterType::Pointer conjugateFilter = RealImageToComplexFilterType::New();
  conjugateFilter->SetInput1(realFilter->GetOutput());
  conjugateFilter->SetInput2(flipSignFilter->GetOutput());


  // The conjugate product of the spectrum
   typedef itk::MultiplyImageFilter< SpectralImageType,
   typedef itk::MultiplyImageFilter< SpectralImageType,
                                    SpectralImageType,
    SpectralImageType,
                                    SpectralImageType >  MultiplyFilterType;
    SpectralImageType >  MultiplyFilterType;
 
   MultiplyFilterType::Pointer multiplyFilter = MultiplyFilterType::New();
   MultiplyFilterType::Pointer multiplyFilter = MultiplyFilterType::New();
  multiplyFilter->SetInput1( fixedFFTFilter->GetOutput() );
  multiplyFilter->SetInput2( conjugateFilter->GetOutput() );


   multiplyFilter->SetInput1( fftFilter1->GetOutput() );
   // IFFT
   multiplyFilter->SetInput2( fftFilter2->GetOutput() );
#if ITK_VERSION_MAJOR < 4
 
   typedef itk::VnlFFTComplexConjugateToRealImageFilter< SpectralImageType > IFFTFilterType;
   typedef itk::VnlFFTComplexConjugateToRealImageFilter<
#else
    InputPixelType, Dimension >  IFFTFilterType;
   typedef itk::VnlInverseFFTImageFilter< SpectralImageType >  IFFTFilterType;
 
#endif
   IFFTFilterType::Pointer fftInverseFilter = IFFTFilterType::New();
   IFFTFilterType::Pointer fftInverseFilter = IFFTFilterType::New();
   fftInverseFilter->SetInput( multiplyFilter->GetOutput() );
   fftInverseFilter->SetInput( multiplyFilter->GetOutput() );


   typedef itk::ImageFileWriter< InputImageType > WriterType;
  // Write the spectrum
   WriterType::Pointer writer = WriterType::New();
  typedef itk::RescaleIntensityImageFilter< FloatImageType,  UnsignedCharImageType > RescaleFilterType;
   writer->SetFileName( argv[3] );
  RescaleFilterType::Pointer  rescaler =  RescaleFilterType::New();
   writer->SetInput( fftInverseFilter->GetOutput() );
  rescaler->SetInput( fftInverseFilter->GetOutput() );
  rescaler->SetOutputMinimum(0);
  rescaler->SetOutputMaximum(255);
  rescaler->Update();
   
   typedef itk::ImageFileWriter< UnsignedCharImageType > WriterType;
   WriterType::Pointer writer = WriterType::New();
   writer->SetFileName( "CrossCorr.png" );
   writer->SetInput( rescaler->GetOutput() );
  writer->Update();


   try
   typedef itk::MinimumMaximumImageCalculator <UnsignedCharImageType>
    {
     ImageCalculatorFilterType;
    writer->Update();
    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "Error writing the real image: " << std::endl;
    std::cerr << excp << std::endl;
     return EXIT_FAILURE;
    }


  ImageCalculatorFilterType::Pointer imageCalculatorFilter
    = ImageCalculatorFilterType::New ();
  imageCalculatorFilter->SetImage(rescaler->GetOutput());
  imageCalculatorFilter->Compute();
 
  UnsignedCharImageType::IndexType maximumLocation = imageCalculatorFilter->GetIndexOfMaximum();
  std::cout << maximumLocation << std::endl; // should be (17,15)
 
  /*
  if ypeak < size(I,1)/2 ypeak = -(ypeak-1);
  else ypeak = size(I,1) - (ypeak-1);
  end
  if xpeak < size(I,2)/2 xpeak = -(xpeak-1);
  else xpeak = size(I,2) - (xpeak-1);
  end
  */
 
   return EXIT_SUCCESS;
   return EXIT_SUCCESS;
}
}
</source>
</source>


==CMakeLists.txt==
{{ITKCMakeLists|{{SUBPAGENAME}}}}
<source lang="cmake">
cmake_minimum_required(VERSION 2.6)
 
project(CrossCorrelationInFourierDomain)
 
find_package(ITK REQUIRED)
include(${ITK_USE_FILE})
 
add_executable(CrossCorrelationInFourierDomain CrossCorrelationInFourierDomain.cxx )
target_link_libraries(CrossCorrelationInFourierDomain ITKIO ITKCommon)
</source>

Latest revision as of 18:11, 25 December 2012

In ITKv4, VnlFFTRealToComplexConjugateImageFilter was renamed VnlForwardFFTImageFilter and VnlFFTComplexConjugateToRealImageFilter was renamed VnlInverseFFTImageFilter.

CrossCorrelationInFourierDomain.cxx

#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"

#if ITK_VERSION_MAJOR < 4
#include "itkVnlFFTRealToComplexConjugateImageFilter.h"
#include "itkVnlFFTComplexConjugateToRealImageFilter.h"
#else
#include "itkVnlForwardFFTImageFilter.h"
#include "itkVnlInverseFFTImageFilter.h"
#endif
#include "itkComplexToRealImageFilter.h"
#include "itkComplexToImaginaryImageFilter.h"
#include "itkMultiplyImageFilter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkFFTShiftImageFilter.h"
#include "itkMinimumMaximumImageCalculator.h"

#if ITK_VERSION_MAJOR < 4
#include "itkMultiplyByConstantImageFilter.h"
#include "itkRealAndImaginaryToComplexImageFilter.h"
#else
#include "itkComposeImageFilter.h"
#endif

int main(int argc, char*argv[])
{
  const    unsigned int    Dimension = 2;
  typedef  float                                  PixelType;
  typedef itk::Image< PixelType, Dimension >      FloatImageType;
  typedef itk::Image< unsigned char, Dimension >  UnsignedCharImageType;

  if( argc < 3 )
    {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];
    std::cerr << " FixedImage MovingImage"<< std::endl;;
    return EXIT_FAILURE;
    }
  std::string fixedImageFilename = argv[1];
  std::string movingImageFilename = argv[2];

  // Read the input images
  typedef itk::ImageFileReader< FloatImageType  > ImageReaderType;
  ImageReaderType::Pointer  fixedImageReader  = ImageReaderType::New();
  fixedImageReader->SetFileName( fixedImageFilename );
  fixedImageReader->Update();
  
  ImageReaderType::Pointer movingImageReader = ImageReaderType::New();
  movingImageReader->SetFileName( movingImageFilename );
  movingImageReader->Update();

  // Shift the input images
  typedef itk::FFTShiftImageFilter< FloatImageType, FloatImageType > FFTShiftFilterType;
  FFTShiftFilterType::Pointer fixedFFTShiftFilter = FFTShiftFilterType::New();
  fixedFFTShiftFilter->SetInput(fixedImageReader->GetOutput());
  fixedFFTShiftFilter->Update();

  FFTShiftFilterType::Pointer movingFFTShiftFilter = FFTShiftFilterType::New();
  movingFFTShiftFilter->SetInput(movingImageReader->GetOutput());
  movingFFTShiftFilter->Update();
  
  // Compute the FFT of the input
#if ITK_VERSION_MAJOR < 4
  typedef itk::VnlFFTRealToComplexConjugateImageFilter< FloatImageType >  FFTFilterType;
#else
  typedef itk::VnlForwardFFTImageFilter< FloatImageType >  FFTFilterType;
#endif
  FFTFilterType::Pointer fixedFFTFilter = FFTFilterType::New();
  fixedFFTFilter->SetInput( fixedFFTShiftFilter->GetOutput() );
  fixedFFTFilter->Update();
  
  FFTFilterType::Pointer movingFFTFilter = FFTFilterType::New();
  movingFFTFilter->SetInput( movingFFTShiftFilter->GetOutput() );
  
  typedef FFTFilterType::OutputImageType    SpectralImageType;

  // Take the conjugate of the fftFilterMoving
  // Extract the real part
  typedef itk::ComplexToRealImageFilter<SpectralImageType, FloatImageType> RealFilterType;
  RealFilterType::Pointer realFilter = RealFilterType::New();
  realFilter->SetInput(movingFFTFilter->GetOutput());

  // Extract the imaginary part
  typedef itk::ComplexToImaginaryImageFilter<SpectralImageType, FloatImageType> ImaginaryFilterType;
  ImaginaryFilterType::Pointer imaginaryFilter = ImaginaryFilterType::New();
  imaginaryFilter->SetInput(movingFFTFilter->GetOutput());

  // Flip the sign of the imaginary and combine with the real part again
#if ITK_VERSION_MAJOR < 4
  typedef itk::MultiplyByConstantImageFilter<FloatImageType,PixelType,FloatImageType> MultiplyConstantFilterType;
#else
  typedef itk::MultiplyImageFilter<FloatImageType,FloatImageType,FloatImageType> MultiplyConstantFilterType;
#endif

  MultiplyConstantFilterType::Pointer flipSignFilter = MultiplyConstantFilterType::New();
#if ITK_VERSION_MAJOR < 4
  flipSignFilter->SetConstant(-1);
#else
  flipSignFilter->SetConstant2(-1);
#endif
  flipSignFilter->SetInput(imaginaryFilter->GetOutput());
#if ITK_VERSION_MAJOR < 4
  typedef itk::RealAndImaginaryToComplexImageFilter<FloatImageType> RealImageToComplexFilterType;
#else
  typedef itk::ComposeImageFilter<FloatImageType, SpectralImageType> RealImageToComplexFilterType;
#endif
  RealImageToComplexFilterType::Pointer conjugateFilter = RealImageToComplexFilterType::New();
  conjugateFilter->SetInput1(realFilter->GetOutput());
  conjugateFilter->SetInput2(flipSignFilter->GetOutput());

  // The conjugate product of the spectrum
  typedef itk::MultiplyImageFilter< SpectralImageType,
    SpectralImageType,
    SpectralImageType >  MultiplyFilterType;
  MultiplyFilterType::Pointer multiplyFilter = MultiplyFilterType::New();
  multiplyFilter->SetInput1( fixedFFTFilter->GetOutput() );
  multiplyFilter->SetInput2( conjugateFilter->GetOutput() );

  // IFFT
#if ITK_VERSION_MAJOR < 4
  typedef itk::VnlFFTComplexConjugateToRealImageFilter< SpectralImageType >  IFFTFilterType;
#else
  typedef itk::VnlInverseFFTImageFilter< SpectralImageType >  IFFTFilterType;
#endif
  IFFTFilterType::Pointer fftInverseFilter = IFFTFilterType::New();
  fftInverseFilter->SetInput( multiplyFilter->GetOutput() );

  // Write the spectrum
  typedef itk::RescaleIntensityImageFilter< FloatImageType,  UnsignedCharImageType > RescaleFilterType;
  RescaleFilterType::Pointer  rescaler =  RescaleFilterType::New();
  rescaler->SetInput( fftInverseFilter->GetOutput() );
  rescaler->SetOutputMinimum(0);
  rescaler->SetOutputMaximum(255);
  rescaler->Update();
    
  typedef itk::ImageFileWriter< UnsignedCharImageType >  WriterType;
  WriterType::Pointer writer =  WriterType::New();
  writer->SetFileName( "CrossCorr.png" );
  writer->SetInput( rescaler->GetOutput() );
  writer->Update();

  typedef itk::MinimumMaximumImageCalculator <UnsignedCharImageType>
    ImageCalculatorFilterType;

  ImageCalculatorFilterType::Pointer imageCalculatorFilter
    = ImageCalculatorFilterType::New ();
  imageCalculatorFilter->SetImage(rescaler->GetOutput());
  imageCalculatorFilter->Compute();
  
  UnsignedCharImageType::IndexType maximumLocation = imageCalculatorFilter->GetIndexOfMaximum();
  std::cout << maximumLocation << std::endl; // should be (17,15)
  
  /*
  if ypeak < size(I,1)/2 ypeak = -(ypeak-1);
  else ypeak = size(I,1) - (ypeak-1);
  end
  if xpeak < size(I,2)/2 xpeak = -(xpeak-1);
  else xpeak = size(I,2) - (xpeak-1);
  end
  */
  
  return EXIT_SUCCESS;
}

CMakeLists.txt

cmake_minimum_required(VERSION 3.9.5)

project(CrossCorrelationInFourierDomain)

find_package(ITK REQUIRED)
include(${ITK_USE_FILE})
if (ITKVtkGlue_LOADED)
  find_package(VTK REQUIRED)
  include(${VTK_USE_FILE})
endif()

add_executable(CrossCorrelationInFourierDomain MACOSX_BUNDLE CrossCorrelationInFourierDomain.cxx)

if( "${ITK_VERSION_MAJOR}" LESS 4 )
  target_link_libraries(CrossCorrelationInFourierDomain ITKReview ${ITK_LIBRARIES})
else( "${ITK_VERSION_MAJOR}" LESS 4 )
  target_link_libraries(CrossCorrelationInFourierDomain ${ITK_LIBRARIES})
endif( "${ITK_VERSION_MAJOR}" LESS 4 )

Download and Build CrossCorrelationInFourierDomain

Click here to download CrossCorrelationInFourierDomain and its CMakeLists.txt file. Once the tarball CrossCorrelationInFourierDomain.tar has been downloaded and extracted,

cd CrossCorrelationInFourierDomain/build
  • If ITK is installed:
cmake ..
  • If ITK is not installed but compiled on your system, you will need to specify the path to your ITK build:
cmake -DITK_DIR:PATH=/home/me/itk_build ..

Build the project:

make

and run it:

./CrossCorrelationInFourierDomain

WINDOWS USERS PLEASE NOTE: Be sure to add the ITK bin directory to your path. This will resolve the ITK dll's at run time.

Building All of the Examples

Many of the examples in the ITK Wiki Examples Collection require VTK. You can build all of the the examples by following these instructions. If you are a new VTK user, you may want to try the Superbuild which will build a proper ITK and VTK.

ItkVtkGlue

ITK >= 4

For examples that use QuickView (which depends on VTK), you must have built ITK with Module_ITKVtkGlue=ON.

ITK < 4

Some of the ITK Examples require VTK to display the images. If you download the entire ITK Wiki Examples Collection, the ItkVtkGlue directory will be included and configured. If you wish to just build a few examples, then you will need to download ItkVtkGlue and build it. When you run cmake it will ask you to specify the location of the ItkVtkGlue binary directory.