ITK/Examples/Broken/Images/NormalizedCorrelationImageFilterMasked

NormalizedCorrelationImageFilterMasked.cxx

<source lang="cpp">

1. include "itkImage.h"
2. include "itkImageFileReader.h"
3. include "itkNormalizedCorrelationImageFilter.h"
4. include "itkRegionOfInterestImageFilter.h"
5. include "itkImageKernelOperator.h"
6. include "itkRescaleIntensityImageFilter.h"
7. include "itkImageFileWriter.h"
8. include "itkMinimumMaximumImageCalculator.h"

1. include <iostream>
2. include <string>

typedef itk::Image<float, 2> ImageType;

//typedef itk::Image<float, 2> FloatImageType; //typedef itk::Image<unsigned char, 2> UnsignedCharImageType;

void CreateImage(ImageType::Pointer image); void CreateImageOfSquare(ImageType::Pointer image, const itk::Index<2>& cornerOfSquare); void WriteImage(ImageType::Pointer image, const std::string& filename); void FillRegion(ImageType::Pointer image, const itk::ImageRegion<2>& region, ImageType::PixelType value);

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

 // Setup mask
 ImageType::Pointer mask = ImageType::New();
 CreateImage(mask);
 
 itk::Index<2> maskIndex;
 maskIndex[0] = mask->GetLargestPossibleRegion().GetSize()[0]/2;
 maskIndex[1] = 0;
 
 itk::Size<2> maskSize;
 maskSize[0] = mask->GetLargestPossibleRegion().GetSize()[0]/2 + 1;
 maskSize[1] = mask->GetLargestPossibleRegion().GetSize()[1];
 
 itk::ImageRegion<2> maskRegion(maskIndex, maskSize);
 FillRegion(mask, maskRegion, 255);
 WriteImage(mask, "mask.mha");

 // Setup image1
 ImageType::Pointer image1 = ImageType::New();
 itk::Index<2> cornerOfSquare1;
 cornerOfSquare1[0] = 3;
 cornerOfSquare1[1] = 8;
 CreateImageOfSquare(image1, cornerOfSquare1);
 WriteImage(image1, "image1.mha");
 
 // Setup image2
 itk::Index<2> offset;
 offset[0] = 20;
 offset[1] = 6;
 
 ImageType::Pointer image2 = ImageType::New();
 itk::Index<2> cornerOfSquare2;
 cornerOfSquare2[0] = cornerOfSquare1[0] + offset[0];
 cornerOfSquare2[1] = cornerOfSquare1[1] + offset[1];
 CreateImageOfSquare(image2, cornerOfSquare2);
 FillRegion(image2, maskRegion, 122); // If this line is uncommented, the result is infinity!?
 WriteImage(image2, "image2.mha");

 // Perform normalized correlation
 // <input type, mask type, output type>
 typedef itk::NormalizedCorrelationImageFilter<ImageType, ImageType, ImageType> CorrelationFilterType;

 itk::ImageKernelOperator<float> kernelOperator;
 kernelOperator.SetImageKernel(image1);

 // The radius of the kernel must be the radius of the patch, NOT the size of the patch
 itk::Size<2> radius;
 radius[0] = image1->GetLargestPossibleRegion().GetSize()[0]/2;
 radius[1] = image1->GetLargestPossibleRegion().GetSize()[1]/2;

 if(radius[0] % 2 == 0 || radius[1] % 2 == 0)
   {
   std::cerr << "Input must have odd dimensions!" << std::endl;
   return EXIT_FAILURE;
   }

 kernelOperator.CreateToRadius(radius);

 CorrelationFilterType::Pointer correlationFilter = CorrelationFilterType::New();
 correlationFilter->SetInput(image2);
 //correlationFilter->SetMaskImage(mask);
 correlationFilter->SetTemplate(kernelOperator);
 correlationFilter->Update();

 WriteImage(correlationFilter->GetOutput(), "correlation.mha");

 typedef itk::MinimumMaximumImageCalculator <ImageType> MinimumMaximumImageCalculatorType;

 MinimumMaximumImageCalculatorType::Pointer minimumMaximumImageCalculatorFilter = MinimumMaximumImageCalculatorType::New ();
 minimumMaximumImageCalculatorFilter->SetImage(correlationFilter->GetOutput());
 minimumMaximumImageCalculatorFilter->Compute();

 itk::Index<2> maximumCorrelationPatchCenter = minimumMaximumImageCalculatorFilter->GetIndexOfMaximum();
 //std::cout << "Maximum location: " << maximumCorrelationPatchCenter << std::endl;
 std::cout << "Maximum location fixed: " << maximumCorrelationPatchCenter - radius << std::endl; // This is the value we expect!
 std::cout << "Maximum value: " << minimumMaximumImageCalculatorFilter->GetMaximum() << std::endl; // If the images can be perfectly aligned, the value is 1

 return EXIT_SUCCESS;

}

void CreateImage(ImageType::Pointer image) {

 ImageType::IndexType start;
 start.Fill(0);

 ImageType::SizeType size;
 size.Fill(51);

 ImageType::RegionType region(start,size);

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

}

void CreateImageOfSquare(ImageType::Pointer image, const itk::Index<2>& cornerOfSquare) {

 ImageType::IndexType start;
 start.Fill(0);

 ImageType::SizeType size;
 size.Fill(51);

 ImageType::RegionType region(start,size);

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

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

 unsigned int squareSize = 8;

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

   ++imageIterator;
   }

}

void WriteImage(ImageType::Pointer image, const std::string& filename) {

 typedef  itk::ImageFileWriter< ImageType  > WriterType;
 WriterType::Pointer writer = WriterType::New();
 writer->SetFileName(filename);
 writer->SetInput(image);
 writer->Update();

}

void FillRegion(ImageType::Pointer image, const itk::ImageRegion<2>& region, ImageType::PixelType value) {

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

 while(!imageIterator.IsAtEnd())
   {
   imageIterator.Set(value);

   ++imageIterator;
   }

}

</source>

CMakeLists.txt

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

project(NormalizedCorrelationImageFilterMasked)

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

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

else()

 find_package(ItkVtkGlue REQUIRED)
 include(${ItkVtkGlue_USE_FILE})
 set(Glue ItkVtkGlue)

endif()

add_executable(NormalizedCorrelationImageFilterMasked MACOSX_BUNDLE NormalizedCorrelationImageFilterMasked.cxx) target_link_libraries(NormalizedCorrelationImageFilterMasked

 ${Glue}  ${VTK_LIBRARIES} ${ITK_LIBRARIES})

</syntaxhighlight>

Download and Build NormalizedCorrelationImageFilterMasked

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

cd NormalizedCorrelationImageFilterMasked/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:

./NormalizedCorrelationImageFilterMasked

WINDOWS USERS PLEASE NOTE: Be sure to add the VTK and ITK bin directories to your path. This will resolve the VTK and 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.