itkdiffeomorphicdemonsregistrationfiltertest.cxx

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/*=========================================================================

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: itkDiffeomorphicDemonsRegistrationFilterTest.cxx,v $
  Language:  C++
  Date:      $Date: 2008-07-12 23:58:17 $
  Version:   $Revision: 1.6 $

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even 
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
     PURPOSE.  See the above copyright notices for more information.

=========================================================================*/
#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif

#include "itkDiffeomorphicDemonsRegistrationFilter.h"

#include "itkIndex.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkWarpImageFilter.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
#include "itkCommand.h"
#include "vnl/vnl_math.h"
#include "itkVectorCastImageFilter.h"
#include "itkImageFileWriter.h"


namespace{
// The following class is used to support callbacks
// on the filter in the pipeline that follows later
template<typename TRegistration>
class ShowProgressObject
{
public:
  ShowProgressObject(TRegistration* o)
    {m_Process = o;}
  void ShowProgress()
    {
    std::cout << "Progress: " << m_Process->GetProgress() << "  ";
    std::cout << "Iter: " << m_Process->GetElapsedIterations() << "  ";
    std::cout << "Metric: "   << m_Process->GetMetric()   << "  ";
    std::cout << "RMSChange: " << m_Process->GetRMSChange() << "  ";
    std::cout << std::endl;
    }
  typename TRegistration::Pointer m_Process;
};
}

// Template function to fill in an image with a circle.
template <class TImage>
void
FillWithCircle(
TImage * image,
double * center,
double radius,
typename TImage::PixelType foregnd,
typename TImage::PixelType backgnd )
{

  typedef itk::ImageRegionIteratorWithIndex<TImage> Iterator;
  Iterator it( image, image->GetBufferedRegion() );
  it.Begin();
    
  typename TImage::IndexType index;
  double r2 = vnl_math_sqr( radius );

  for( ; !it.IsAtEnd(); ++it )
    {
    index = it.GetIndex();
    double distance = 0;
    for( unsigned int j = 0; j < TImage::ImageDimension; j++ )
      {
      distance += vnl_math_sqr((double) index[j] - center[j]);
      }
    if( distance <= r2 ) it.Set( foregnd );
    else it.Set( backgnd ); 
    }

}


// Template function to copy image regions
template <class TImage>
void
CopyImageBuffer(
TImage *input,
TImage *output )
{
  typedef itk::ImageRegionIteratorWithIndex<TImage> Iterator;
  Iterator inIt( input, output->GetBufferedRegion() );
  Iterator outIt( output, output->GetBufferedRegion() );
  for( ; !inIt.IsAtEnd(); ++inIt, ++outIt )
    {
    outIt.Set( inIt.Get() );
    }

}

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

  if( argc < 9 )
    {
    std::cerr << "Missing arguments" << std::endl;
    std::cerr << "Usage:" << std::endl;
    std::cerr << argv[0] << std::endl;
    std::cerr << "GradientType [0=Symmetric,1=Fixed,2=WarpedMoving,3=MappedMoving]" << std::endl;
    std::cerr << "UseFirstOrderExp [0=No,1=Yes]" << std::endl;
    std::cerr << "Intensity Difference Threshold (double)" << std::endl;
    std::cerr << "Maximum Update step length (double)" << std::endl;
    std::cerr << "Maximum number of iterations (int)" << std::endl;
    std::cerr << "Standard deviations (double)" << std::endl;
    std::cerr << "Maximum error (double)" << std::endl;
    std::cerr << "Maximum kernel width (int)" << std::endl;
    return EXIT_FAILURE;
    }

  typedef unsigned char PixelType;
  enum {ImageDimension = 2};
  typedef itk::Image<PixelType,ImageDimension> ImageType;  
  typedef itk::Vector<float,ImageDimension> VectorType;
  typedef itk::Image<VectorType,ImageDimension> FieldType;
  typedef itk::Image<VectorType::ValueType,ImageDimension> FloatImageType;
  typedef ImageType::IndexType  IndexType;
  typedef ImageType::SizeType   SizeType;
  typedef ImageType::RegionType RegionType;

  //--------------------------------------------------------
  std::cout << "Generate input images and initial deformation field";
  std::cout << std::endl;

  unsigned long sizeArray[ImageDimension] = { 128, 128 };
  SizeType size;
  size.SetSize( sizeArray );

  IndexType index;
  index.Fill( 0 );
 
  RegionType region;
  region.SetSize( size );
  region.SetIndex( index );
  
  ImageType::Pointer moving = ImageType::New();
  ImageType::Pointer fixed = ImageType::New();
  FieldType::Pointer initField = FieldType::New();

  moving->SetLargestPossibleRegion( region );
  moving->SetBufferedRegion( region );
  moving->Allocate();

  fixed->SetLargestPossibleRegion( region );
  fixed->SetBufferedRegion( region );
  fixed->Allocate();
  
  initField->SetLargestPossibleRegion( region );
  initField->SetBufferedRegion( region );
  initField->Allocate();

  double center[ImageDimension];
  double radius;
  PixelType fgnd = 250;
  PixelType bgnd = 15;

  // fill moving with circle 
  center[0] = 64; center[1] = 64; radius = 30;
  FillWithCircle<ImageType>( moving, center, radius, fgnd, bgnd );

  // fill fixed with circle
  center[0] = 62; center[1] = 64; radius = 30;
  FillWithCircle<ImageType>( fixed, center, radius, fgnd, bgnd );

  // fill initial deformation with zero vectors
  VectorType zeroVec;
  zeroVec.Fill( 0.0 );
  initField->FillBuffer( zeroVec );

  typedef itk::VectorCastImageFilter<FieldType,FieldType> CasterType;
  CasterType::Pointer caster = CasterType::New();
  caster->SetInput( initField );
  caster->InPlaceOff();

  //-------------------------------------------------------------
  std::cout << "Run registration and warp moving" << std::endl;

  typedef itk::DiffeomorphicDemonsRegistrationFilter<
    ImageType,ImageType,FieldType>                      RegistrationType;

  RegistrationType::Pointer registrator = RegistrationType::New();

  registrator->SetInitialDeformationField( caster->GetOutput() );

  registrator->SetMovingImage( moving );
  registrator->SetFixedImage( fixed );

  const double intensityDifferenceThreshold = atof( argv[3] );
  const double maximumUpdateStepLength = atof( argv[4] );
  const unsigned int numberOfIterations = atoi( argv[5] );
  const double standardDeviations = atof( argv[6] );
  const double maximumError = atof( argv[7] );
  const unsigned int maximumKernelWidth = atoi( argv[8] );

  registrator->SetIntensityDifferenceThreshold( intensityDifferenceThreshold );
  registrator->SetMaximumUpdateStepLength( maximumUpdateStepLength );
  registrator->SetNumberOfIterations( numberOfIterations );
  registrator->SetStandardDeviations( standardDeviations );
  registrator->SetMaximumError( maximumError );
  registrator->SetMaximumKernelWidth( maximumKernelWidth );

  const int gradientType = atoi( argv[1] );

  typedef RegistrationType::DemonsRegistrationFunctionType FunctionType;

  switch( gradientType )
    {
    case 0:
      registrator->SetUseGradientType( FunctionType::Symmetric );
      break;
    case 1:
      registrator->SetUseGradientType( FunctionType::Fixed );
      break;
    case 2:
      registrator->SetUseGradientType( FunctionType::WarpedMoving );
      break;
    case 3:
      registrator->SetUseGradientType( FunctionType::MappedMoving );
      break;
    }

  std::cout << "GradientType = " << registrator->GetUseGradientType() << std::endl;

  const int useFirstOrderExponential = atoi( argv[2] );

  if( useFirstOrderExponential == 0 )
    {
    registrator->SetUseFirstOrderExp( false );
    }
  else
    {
    registrator->SetUseFirstOrderExp( true );
    }


  // turn on inplace execution
  registrator->InPlaceOn();


  FunctionType * fptr;
  fptr = dynamic_cast<FunctionType *>(
    registrator->GetDifferenceFunction().GetPointer() );
  fptr->Print( std::cout );

  // exercise other member variables
  std::cout << "No. Iterations: " << registrator->GetNumberOfIterations() << std::endl;
  std::cout << "Max. kernel error: " << registrator->GetMaximumError() << std::endl;
  std::cout << "Max. kernel width: " << registrator->GetMaximumKernelWidth() << std::endl;
  
  double v[ImageDimension];
  for ( unsigned int j = 0; j < ImageDimension; j++ )
    {
    v[j] = registrator->GetStandardDeviations()[j];
    }
  registrator->SetStandardDeviations( v );

  typedef ShowProgressObject<RegistrationType> ProgressType;
  ProgressType progressWatch(registrator);
  itk::SimpleMemberCommand<ProgressType>::Pointer command;
  command = itk::SimpleMemberCommand<ProgressType>::New();
  command->SetCallbackFunction(&progressWatch,
                               &ProgressType::ShowProgress);
  registrator->AddObserver( itk::ProgressEvent(), command);
 
  // warp moving image
  typedef itk::WarpImageFilter<ImageType,ImageType,FieldType> WarperType;
  WarperType::Pointer warper = WarperType::New();

  typedef WarperType::CoordRepType CoordRepType;
  typedef itk::NearestNeighborInterpolateImageFunction<ImageType,CoordRepType>
    InterpolatorType;
  InterpolatorType::Pointer interpolator = InterpolatorType::New();
  

  warper->SetInput( moving );
  warper->SetDeformationField( registrator->GetOutput() );
  warper->SetInterpolator( interpolator );
  warper->SetOutputSpacing( fixed->GetSpacing() );
  warper->SetOutputOrigin( fixed->GetOrigin() );

  warper->Print( std::cout );

  warper->Update();
 
  // ---------------------------------------------------------
  std::cout << "Compare warped moving and fixed." << std::endl;

  // compare the warp and fixed images
  itk::ImageRegionIterator<ImageType> fixedIter( fixed,
      fixed->GetBufferedRegion() );
  itk::ImageRegionIterator<ImageType> warpedIter( warper->GetOutput(),
      fixed->GetBufferedRegion() );

  unsigned int numPixelsDifferent = 0;
  while( !fixedIter.IsAtEnd() )
    {
    if( fixedIter.Get() != warpedIter.Get() )
      {
      numPixelsDifferent++;
      }
    ++fixedIter;
    ++warpedIter;
    }

  typedef itk::ImageFileWriter< ImageType > WriterType;

  WriterType::Pointer writer1 = WriterType::New();
  WriterType::Pointer writer2 = WriterType::New();
  WriterType::Pointer writer3 = WriterType::New();

  writer1->SetFileName("fixedImage.mha");
  writer2->SetFileName("movingImage.mha");
  writer3->SetFileName("registeredImage.mha");

  writer1->SetInput( fixed );
  writer2->SetInput( moving );
  writer3->SetInput( warper->GetOutput() );

  writer1->Update();
  writer2->Update();
  writer3->Update();

  std::cout << "Number of pixels different: " << numPixelsDifferent; 
  std::cout << std::endl;

  const unsigned int maximumNumberOfDifferentPixels = atoi( argv[9] );

  if( numPixelsDifferent > maximumNumberOfDifferentPixels )
    {
    std::cout << "Test failed - too many pixels different." << std::endl;
    return EXIT_FAILURE;
    }

  registrator->Print( std::cout );

  // -----------------------------------------------------------
  std::cout << "Test running registrator without initial deformation field.";
  std::cout << std::endl;

  bool passed = true;
  try
    {
    registrator->SetInput( NULL );
    registrator->SetNumberOfIterations( 2 );
    registrator->Update();
    }
  catch( itk::ExceptionObject& err )
    {
    std::cout << "Unexpected error." << std::endl;
    std::cout << err << std::endl;
    passed = false;
    }

  if ( !passed )
    {
    std::cout << "Test failed" << std::endl;
    return EXIT_FAILURE;
    }

  //--------------------------------------------------------------
  std::cout << "Test exception handling." << std::endl;

  std::cout << "Test NULL moving image. " << std::endl;
  passed = false;
  try
    {
    registrator->SetInput( caster->GetOutput() );
    registrator->SetMovingImage( NULL );
    registrator->Update();
    }
  catch( itk::ExceptionObject & err )
    {
    std::cout << "Caught expected error." << std::endl;
    std::cout << err << std::endl;
    passed = true;
    }
  
  if ( !passed )
    {
    std::cout << "Test failed" << std::endl;
    return EXIT_FAILURE;
    }
  registrator->SetMovingImage( moving );
  registrator->ResetPipeline();

  std::cout << "Test NULL moving image interpolator. " << std::endl;
  passed = false;
  try
    {
    fptr = dynamic_cast<FunctionType *>(
      registrator->GetDifferenceFunction().GetPointer() );
    fptr->SetMovingImageInterpolator( NULL );
    registrator->SetInput( initField );
    registrator->Update();
    }
  catch( itk::ExceptionObject & err )
    {
    std::cout << "Caught expected error." << std::endl;
    std::cout << err << std::endl;
    passed = true;
    }
  
  if ( !passed )
    {
    std::cout << "Test failed" << std::endl;
    return EXIT_FAILURE;
    }

  std::cout << "Test passed" << std::endl;
  return EXIT_SUCCESS;
  

}