ITK/Examples/Registration/WarpImageFilter

WarpImageFilter.cxx

<source lang="cpp">

1. include "itkImageFileReader.h"
2. include "itkImageFileWriter.h"
3. include "itkImage.h"
4. include "itkVector.h"
5. include "itkDeformationFieldSource.h"
6. include "itkDeformationFieldTransform.h"
7. include "itkWarpImageFilter.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[]) {

 typedef   float          VectorComponentType;

 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);
 
 typedef itk::DeformationFieldSource<DeformationFieldType>  DeformationFieldSourceType;
 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();
 }
 

 typedef itk::WarpImageFilter< ImageType,
                               ImageType,
                               DeformationFieldType  >  WarpImageFilterType;

 WarpImageFilterType::Pointer warpImageFilter = WarpImageFilterType::New();

 typedef itk::LinearInterpolateImageFunction<ImageType, double >  InterpolatorType;

 InterpolatorType::Pointer interpolator = InterpolatorType::New();
 warpImageFilter->SetInterpolator( interpolator );
 warpImageFilter->SetOutputSpacing( deformationFieldSource->GetOutput()->GetSpacing() );
 warpImageFilter->SetOutputOrigin(  deformationFieldSource->GetOutput()->GetOrigin() );
 warpImageFilter->SetDeformationField( deformationFieldSource->GetOutput() );
 warpImageFilter->SetInput( movingImage );
 warpImageFilter->Update();

 // Write the output
 typedef itk::ImageFileWriter<  ImageType  > WriterType;
 WriterType::Pointer writer = WriterType::New();
 writer->SetInput (  warpImageFilter->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(WarpImageFilter)

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

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

endif()

add_executable(WarpImageFilter MACOSX_BUNDLE WarpImageFilter.cxx)

if( "${ITK_VERSION_MAJOR}" LESS 4 )

 target_link_libraries(WarpImageFilter ITKReview ${ITK_LIBRARIES})

else( "${ITK_VERSION_MAJOR}" LESS 4 )

 target_link_libraries(WarpImageFilter ${ITK_LIBRARIES})

endif( "${ITK_VERSION_MAJOR}" LESS 4 )

</syntaxhighlight>

Download and Build WarpImageFilter

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

cd WarpImageFilter/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:

./WarpImageFilter

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.