ITK/Examples/Registration/DeformationFieldTransform: Difference between revisions

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</source>
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{{ITKCMakeLists|DeformationFieldTransform|}}
{{ITKCMakeLists|{{SUBPAGENAME}}}}

Latest revision as of 13:07, 25 December 2012

Please note that in ITKv4, DeformationFieldTransform was renamed to DisplacementFieldTransform.

DeformationFieldTransform.cxx

<source lang="cpp">

  1. include "itkImageFileReader.h"
  2. include "itkImageFileWriter.h"
  3. include "itkImage.h"
  4. include "itkVector.h"
  5. if ITK_VERSION_MAJOR < 4
  6. include "itkDeformationFieldTransform.h"
  7. include "itkDeformationFieldSource.h"
  8. else
  9. include "itkVectorLinearInterpolateImageFunction.h"
  10. include "itkDisplacementFieldTransform.h"
  11. include "itkLandmarkDisplacementFieldSource.h"
  12. endif
  13. include "itkResampleImageFilter.h"

const unsigned int Dimension = 2; typedef unsigned char PixelType; typedef itk::Image< PixelType, Dimension > ImageType;

static void CreateFixedImage(ImageType::Pointer image); static void CreateMovingImage(ImageType::Pointer image);

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

  1. if ITK_VERSION_MAJOR < 4
 typedef   float           VectorComponentType;
  1. else
 typedef   double          VectorComponentType;
  1. endif
 typedef   itk::Vector< VectorComponentType, Dimension >    VectorType;
 typedef   itk::Image< VectorType,  Dimension >   DeformationFieldType;

 ImageType::Pointer fixedImage = ImageType::New();
 CreateFixedImage(fixedImage);
 
 ImageType::Pointer movingImage = ImageType::New();
 CreateMovingImage(movingImage);
  1. if ITK_VERSION_MAJOR < 4
 typedef itk::DeformationFieldSource<DeformationFieldType>  DeformationFieldSourceType;
  1. else
 typedef itk::LandmarkDisplacementFieldSource<DeformationFieldType>  DeformationFieldSourceType;
  1. endif
 DeformationFieldSourceType::Pointer deformationFieldSource = DeformationFieldSourceType::New();
 deformationFieldSource->SetOutputSpacing( fixedImage->GetSpacing() );
 deformationFieldSource->SetOutputOrigin(  fixedImage->GetOrigin() );
 deformationFieldSource->SetOutputRegion(  fixedImage->GetLargestPossibleRegion() );
 deformationFieldSource->SetOutputDirection( fixedImage->GetDirection() );

 //  Create source and target landmarks.
 typedef DeformationFieldSourceType::LandmarkContainerPointer   LandmarkContainerPointer;
 typedef DeformationFieldSourceType::LandmarkContainer          LandmarkContainerType;
 typedef DeformationFieldSourceType::LandmarkPointType          LandmarkPointType;

 LandmarkContainerType::Pointer sourceLandmarks = LandmarkContainerType::New();
 LandmarkContainerType::Pointer targetLandmarks = LandmarkContainerType::New();

 LandmarkPointType sourcePoint;
 LandmarkPointType targetPoint;

 sourcePoint[0] = 40;
 sourcePoint[1] = 40;
 targetPoint[0] = 20;
 targetPoint[1] = 20;
 sourceLandmarks->InsertElement( 0, sourcePoint );
 targetLandmarks->InsertElement( 0, targetPoint );

 sourcePoint[0] = 40;
 sourcePoint[1] = 60;
 targetPoint[0] = 20;
 targetPoint[1] = 80;
 sourceLandmarks->InsertElement( 1, sourcePoint );
 targetLandmarks->InsertElement( 1, targetPoint );

 sourcePoint[0] = 60;
 sourcePoint[1] = 40;
 targetPoint[0] = 80;
 targetPoint[1] = 20;
 sourceLandmarks->InsertElement( 2, sourcePoint );
 targetLandmarks->InsertElement( 2, targetPoint );

 sourcePoint[0] = 60;
 sourcePoint[1] = 60;
 targetPoint[0] = 80;
 targetPoint[1] = 80;
 sourceLandmarks->InsertElement( 3, sourcePoint );
 targetLandmarks->InsertElement( 3, targetPoint );

 deformationFieldSource->SetSourceLandmarks( sourceLandmarks.GetPointer() );
 deformationFieldSource->SetTargetLandmarks( targetLandmarks.GetPointer() );
 deformationFieldSource->UpdateLargestPossibleRegion();

 // Write the deformation field
 {
 typedef itk::ImageFileWriter<  DeformationFieldType  > WriterType;
 WriterType::Pointer writer = WriterType::New();
 writer->SetInput (  deformationFieldSource->GetOutput() );
 writer->SetFileName( "deformation.mhd" );
 writer->Update();
 }
  1. if ITK_VERSION_MAJOR < 4
 typedef itk::DeformationFieldTransform<VectorComponentType, 2>  DeformationFieldTransformType;
  1. else
 typedef itk::DisplacementFieldTransform<VectorComponentType, 2>  DeformationFieldTransformType;
  1. endif
 DeformationFieldTransformType::Pointer deformationFieldTransform = DeformationFieldTransformType::New();
  1. if ITK_VERSION_MAJOR < 4
 deformationFieldTransform->SetDeformationField( deformationFieldSource->GetOutput() );
  1. else
 deformationFieldTransform->SetDisplacementField( deformationFieldSource->GetOutput() );
  1. endif
 typedef itk::ResampleImageFilter<ImageType, ImageType, VectorComponentType >    ResampleFilterType;
 ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New();
 resampleFilter->SetInput( movingImage );
 resampleFilter->SetTransform( deformationFieldTransform );
 resampleFilter->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
 resampleFilter->SetOutputOrigin(  fixedImage->GetOrigin() );
 resampleFilter->SetOutputSpacing( fixedImage->GetSpacing() );
 resampleFilter->SetOutputDirection( fixedImage->GetDirection() );
 resampleFilter->SetDefaultPixelValue( 200 );
 resampleFilter->GetOutput();

 // Write the output
 typedef itk::ImageFileWriter<  ImageType  > WriterType;
 WriterType::Pointer writer = WriterType::New();
 writer->SetInput (  resampleFilter->GetOutput() );
 writer->SetFileName( "output.png" );
 writer->Update();
 
 return EXIT_SUCCESS;

}

void CreateFixedImage(ImageType::Pointer image) { 

 // Create a black image with a white square
 ImageType::IndexType start;
 start.Fill(0);

 ImageType::SizeType size;
 size.Fill(100);

 ImageType::RegionType region;
 region.SetSize(size);
 region.SetIndex(start);

 image->SetRegions(region);
 image->Allocate();
 image->FillBuffer(0);

 itk::ImageRegionIterator<ImageType> imageIterator(image,region);

 while(!imageIterator.IsAtEnd())
   {
   if(imageIterator.GetIndex()[0] > 40 && imageIterator.GetIndex()[0] < 60 &&
     imageIterator.GetIndex()[1] > 40 && imageIterator.GetIndex()[1] < 60)
     {
     imageIterator.Set(255);
     }
   ++imageIterator;
   }

 // Write the deformation field
 typedef itk::ImageFileWriter<  ImageType  > WriterType;
 WriterType::Pointer writer = WriterType::New();
 writer->SetInput (  image );
 writer->SetFileName( "fixed.png" );
 writer->Update();

}


void CreateMovingImage(ImageType::Pointer image) { 

 // Create a black image with a white square
 ImageType::IndexType start;
 start.Fill(0);

 ImageType::SizeType size;
 size.Fill(100);

 ImageType::RegionType region;
 region.SetSize(size);
 region.SetIndex(start);

 image->SetRegions(region);
 image->Allocate();
 image->FillBuffer(0);

 itk::ImageRegionIterator<ImageType> imageIterator(image,region);

 while(!imageIterator.IsAtEnd())
   {
   if(imageIterator.GetIndex()[0] > 20 && imageIterator.GetIndex()[0] < 80 &&
     imageIterator.GetIndex()[1] > 20 && imageIterator.GetIndex()[1] < 80)
     {
     imageIterator.Set(100);
     }
   ++imageIterator;
   }

 // Write the deformation field
 typedef itk::ImageFileWriter<  ImageType  > WriterType;
 WriterType::Pointer writer = WriterType::New();
 writer->SetInput (  image );
 writer->SetFileName( "moving.png" );
 writer->Update();

} </source>

CMakeLists.txt

<syntaxhighlight lang="cmake"> cmake_minimum_required(VERSION 3.9.5)

project(DeformationFieldTransform)

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

 find_package(VTK REQUIRED)
 include(${VTK_USE_FILE})

endif()

add_executable(DeformationFieldTransform MACOSX_BUNDLE DeformationFieldTransform.cxx)

if( "${ITK_VERSION_MAJOR}" LESS 4 ) 

 target_link_libraries(DeformationFieldTransform ITKReview ${ITK_LIBRARIES})

else( "${ITK_VERSION_MAJOR}" LESS 4 ) 

 target_link_libraries(DeformationFieldTransform ${ITK_LIBRARIES})

endif( "${ITK_VERSION_MAJOR}" LESS 4 )

</syntaxhighlight>

Download and Build DeformationFieldTransform

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

cd DeformationFieldTransform/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: 

./DeformationFieldTransform

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.

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