ITK/Examples/Broken/Images/NormalizedCorrelationImageFilterMasked: Difference between revisions

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(Created page with "==NormalizedCorrelationImageFilterMasked.cxx== <source lang="cpp"> #include "itkImage.h" #include "itkImageFileReader.h" #include "itkNormalizedCorrelationImageFilter.h" #include...")
 
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==NormalizedCorrelationImageFilterMasked.cxx==
==NormalizedCorrelationImageFilterMasked.cxx==
<source lang="cpp">
<source lang="cpp">
// Maximum value is inf??
#include "itkImage.h"
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileReader.h"
Line 13: Line 15:
#include <string>
#include <string>


typedef itk::Image<float, 2> ImageType;
typedef itk::Image<unsigned char, 2> ImageType;
typedef itk::Image<unsigned char, 2> MaskType;
typedef itk::Image<float, 2> FloatImageType;


//typedef itk::Image<float, 2> FloatImageType;
void CreateMask(MaskType* const mask);
//typedef itk::Image<unsigned char, 2> UnsignedCharImageType;
void CreateImage(ImageType* const image);
void CreateImageOfSquare(ImageType* const image, const itk::Index<2>& cornerOfSquare);


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


int main(int argc, char *argv[])
int main(int argc, char *argv[])
{
{
   // Setup mask
   // Setup mask
   ImageType::Pointer mask = ImageType::New();
   MaskType::Pointer mask = MaskType::New();
   CreateImage(mask);
   CreateMask(mask);
 
 
   itk::Index<2> maskIndex;
   itk::Index<2> maskIndex;
   maskIndex[0] = mask->GetLargestPossibleRegion().GetSize()[0]/2;
   maskIndex[0] = mask->GetLargestPossibleRegion().GetSize()[0]/2;
   maskIndex[1] = 0;
   maskIndex[1] = 0;
 
 
   itk::Size<2> maskSize;
   itk::Size<2> maskSize;
   maskSize[0] = mask->GetLargestPossibleRegion().GetSize()[0]/2 + 1;
   maskSize[0] = mask->GetLargestPossibleRegion().GetSize()[0]/2 + 1;
   maskSize[1] = mask->GetLargestPossibleRegion().GetSize()[1];
   maskSize[1] = mask->GetLargestPossibleRegion().GetSize()[1];
 
 
   itk::ImageRegion<2> maskRegion(maskIndex, maskSize);
   itk::ImageRegion<2> maskRegion(maskIndex, maskSize);
   FillRegion(mask, maskRegion, 255);
   FillRegion(mask.GetPointer(), maskRegion, 255);
   WriteImage(mask, "mask.mha");
   WriteImage(mask.GetPointer(), "mask.mha");


   // Setup image1
   // Setup image1
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   cornerOfSquare1[1] = 8;
   cornerOfSquare1[1] = 8;
   CreateImageOfSquare(image1, cornerOfSquare1);
   CreateImageOfSquare(image1, cornerOfSquare1);
   WriteImage(image1, "image1.mha");
   WriteImage(image1.GetPointer(), "image1.mha");
 
 
   // Setup image2
   // Setup image2
   itk::Index<2> offset;
   itk::Index<2> offset;
   offset[0] = 20;
   offset[0] = 20;
   offset[1] = 6;
   offset[1] = 6;
 
 
   ImageType::Pointer image2 = ImageType::New();
   ImageType::Pointer image2 = ImageType::New();
   itk::Index<2> cornerOfSquare2;
   itk::Index<2> cornerOfSquare2;
Line 59: Line 66:
   cornerOfSquare2[1] = cornerOfSquare1[1] + offset[1];
   cornerOfSquare2[1] = cornerOfSquare1[1] + offset[1];
   CreateImageOfSquare(image2, cornerOfSquare2);
   CreateImageOfSquare(image2, cornerOfSquare2);
   FillRegion(image2, maskRegion, 122); // If this line is uncommented, the result is infinity!?
   FillRegion(image2.GetPointer(), maskRegion, 122); // If this line is uncommented, the result is infinity!?
   WriteImage(image2, "image2.mha");
   WriteImage(image2.GetPointer(), "image2.mha");


   // Perform normalized correlation
   // Create a kernel from an image
  // <input type, mask type, output type>
   itk::ImageKernelOperator<unsigned char> kernelOperator;
  typedef itk::NormalizedCorrelationImageFilter<ImageType, ImageType, ImageType> CorrelationFilterType;
 
   itk::ImageKernelOperator<float> kernelOperator;
   kernelOperator.SetImageKernel(image1);
   kernelOperator.SetImageKernel(image1);


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   kernelOperator.CreateToRadius(radius);
   kernelOperator.CreateToRadius(radius);


  // Perform normalized correlation
  // <input type, mask type, output type>
  typedef itk::NormalizedCorrelationImageFilter<ImageType, MaskType, FloatImageType, unsigned char> CorrelationFilterType;
   CorrelationFilterType::Pointer correlationFilter = CorrelationFilterType::New();
   CorrelationFilterType::Pointer correlationFilter = CorrelationFilterType::New();
   correlationFilter->SetInput(image2);
   correlationFilter->SetInput(image2);
   //correlationFilter->SetMaskImage(mask);
   correlationFilter->SetMaskImage(mask);
   correlationFilter->SetTemplate(kernelOperator);
   correlationFilter->SetTemplate(kernelOperator);
   correlationFilter->Update();
   correlationFilter->Update();
Line 90: Line 97:
   WriteImage(correlationFilter->GetOutput(), "correlation.mha");
   WriteImage(correlationFilter->GetOutput(), "correlation.mha");


   typedef itk::MinimumMaximumImageCalculator <ImageType> MinimumMaximumImageCalculatorType;
  typedef itk::RescaleIntensityImageFilter<FloatImageType, ImageType> RescaleFilterType;
 
  RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
  rescaleFilter->SetInput(correlationFilter->GetOutput());
  rescaleFilter->SetOutputMinimum(0);
  rescaleFilter->SetOutputMaximum(255);
  rescaleFilter->Update();
  WriteImage(rescaleFilter->GetOutput(), "correlation.png");
 
   typedef itk::MinimumMaximumImageCalculator<FloatImageType> MinimumMaximumImageCalculatorType;
   MinimumMaximumImageCalculatorType::Pointer minimumMaximumImageCalculatorFilter = MinimumMaximumImageCalculatorType::New ();
   MinimumMaximumImageCalculatorType::Pointer minimumMaximumImageCalculatorFilter = MinimumMaximumImageCalculatorType::New ();
   minimumMaximumImageCalculatorFilter->SetImage(correlationFilter->GetOutput());
   minimumMaximumImageCalculatorFilter->SetImage(correlationFilter->GetOutput());
Line 97: Line 111:


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


   return EXIT_SUCCESS;
   return EXIT_SUCCESS;
}
}


void CreateImage(ImageType::Pointer image)
void CreateMask(MaskType* const mask)
{
  ImageType::IndexType start;
  start.Fill(0);
 
  ImageType::SizeType size;
  size.Fill(51);
 
  ImageType::RegionType region(start,size);
 
  mask->SetRegions(region);
  mask->Allocate();
  mask->FillBuffer(0);
 
  itk::ImageRegionIterator<MaskType> maskIterator(mask, region);
 
  //unsigned int squareSize = 8;
  unsigned int squareSize = 3;
 
  itk::Index<2> cornerOfSquare = {{3,8}};
 
  while(!maskIterator.IsAtEnd())
    {
    if(maskIterator.GetIndex()[0] > cornerOfSquare[0] &&
      maskIterator.GetIndex()[0] < cornerOfSquare[0] + squareSize &&
      maskIterator.GetIndex()[1] > cornerOfSquare[1] &&
      maskIterator.GetIndex()[1] < cornerOfSquare[1] + squareSize)
      {
      maskIterator.Set(255);
      }
 
    ++maskIterator;
    }
}
 
void CreateImage(ImageType* const image)
{
{
   ImageType::IndexType start;
   ImageType::IndexType start;
Line 119: Line 171:
}
}


void CreateImageOfSquare(ImageType::Pointer image, const itk::Index<2>& cornerOfSquare)
void CreateImageOfSquare(ImageType* const image, const itk::Index<2>& cornerOfSquare)
{
{
   ImageType::IndexType start;
   ImageType::IndexType start;
Line 139: Line 191:
   while(!imageIterator.IsAtEnd())
   while(!imageIterator.IsAtEnd())
     {
     {
     if(imageIterator.GetIndex()[0] > cornerOfSquare[0] && imageIterator.GetIndex()[0] < cornerOfSquare[0] + squareSize &&
     if(imageIterator.GetIndex()[0] > cornerOfSquare[0] &&
      imageIterator.GetIndex()[1] > cornerOfSquare[1] && imageIterator.GetIndex()[1] < cornerOfSquare[1] + squareSize)
      imageIterator.GetIndex()[0] < cornerOfSquare[0] + squareSize &&
      imageIterator.GetIndex()[1] > cornerOfSquare[1] &&
      imageIterator.GetIndex()[1] < cornerOfSquare[1] + squareSize)
       {
       {
       imageIterator.Set(255);
       imageIterator.Set(255);
Line 149: Line 203:
}
}


void WriteImage(ImageType::Pointer image, const std::string& filename)
template <typename TImage>
void WriteImage(const TImage* const image, const std::string& filename)
{
{
   typedef  itk::ImageFileWriter< ImageType  > WriterType;
   typedef  itk::ImageFileWriter<TImage> WriterType;
   WriterType::Pointer writer = WriterType::New();
   typename WriterType::Pointer writer = WriterType::New();
   writer->SetFileName(filename);
   writer->SetFileName(filename);
   writer->SetInput(image);
   writer->SetInput(image);
Line 159: Line 214:
}
}


void FillRegion(ImageType::Pointer image, const itk::ImageRegion<2>& region, ImageType::PixelType value)
template <typename TImage>
void FillRegion(TImage* const image, const itk::ImageRegion<2>& region,
                const typename TImage::PixelType& value)
{
{
   itk::ImageRegionIterator<ImageType> imageIterator(image, region);
   itk::ImageRegionIterator<TImage> imageIterator(image, region);


   while(!imageIterator.IsAtEnd())
   while(!imageIterator.IsAtEnd())

Revision as of 17:50, 26 June 2012

NormalizedCorrelationImageFilterMasked.cxx

<source lang="cpp"> // Maximum value is inf??

  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<unsigned char, 2> ImageType; typedef itk::Image<unsigned char, 2> MaskType; typedef itk::Image<float, 2> FloatImageType;

void CreateMask(MaskType* const mask); void CreateImage(ImageType* const image); void CreateImageOfSquare(ImageType* const image, const itk::Index<2>& cornerOfSquare);

template <typename TImage> void WriteImage(const TImage* const image, const std::string& filename);

template <typename TImage> void FillRegion(TImage* const image, const itk::ImageRegion<2>& region,

               const typename TImage::PixelType& value);

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

 // Setup mask
 MaskType::Pointer mask = MaskType::New();
 CreateMask(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.GetPointer(), maskRegion, 255);
 WriteImage(mask.GetPointer(), "mask.mha");
 // Setup image1
 ImageType::Pointer image1 = ImageType::New();
 itk::Index<2> cornerOfSquare1;
 cornerOfSquare1[0] = 3;
 cornerOfSquare1[1] = 8;
 CreateImageOfSquare(image1, cornerOfSquare1);
 WriteImage(image1.GetPointer(), "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.GetPointer(), maskRegion, 122); // If this line is uncommented, the result is infinity!?
 WriteImage(image2.GetPointer(), "image2.mha");
 // Create a kernel from an image
 itk::ImageKernelOperator<unsigned char> 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);
 // Perform normalized correlation
 // <input type, mask type, output type>
 typedef itk::NormalizedCorrelationImageFilter<ImageType, MaskType, FloatImageType, unsigned char> CorrelationFilterType;
 CorrelationFilterType::Pointer correlationFilter = CorrelationFilterType::New();
 correlationFilter->SetInput(image2);
 correlationFilter->SetMaskImage(mask);
 correlationFilter->SetTemplate(kernelOperator);
 correlationFilter->Update();
 WriteImage(correlationFilter->GetOutput(), "correlation.mha");
 typedef itk::RescaleIntensityImageFilter<FloatImageType, ImageType> RescaleFilterType;
 RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
 rescaleFilter->SetInput(correlationFilter->GetOutput());
 rescaleFilter->SetOutputMinimum(0);
 rescaleFilter->SetOutputMaximum(255);
 rescaleFilter->Update();
 WriteImage(rescaleFilter->GetOutput(), "correlation.png");
 
 typedef itk::MinimumMaximumImageCalculator<FloatImageType> MinimumMaximumImageCalculatorType;
 MinimumMaximumImageCalculatorType::Pointer minimumMaximumImageCalculatorFilter = MinimumMaximumImageCalculatorType::New ();
 minimumMaximumImageCalculatorFilter->SetImage(correlationFilter->GetOutput());
 minimumMaximumImageCalculatorFilter->Compute();
 itk::Index<2> maximumCorrelationPatchCenter = minimumMaximumImageCalculatorFilter->GetIndexOfMaximum();
 // This is the value we expect!
 std::cout << "Maximum location fixed: " << maximumCorrelationPatchCenter - radius << std::endl;
 // If the images can be perfectly aligned, the value is 1
 std::cout << "Maximum value: " << minimumMaximumImageCalculatorFilter->GetMaximum() << std::endl;
 return EXIT_SUCCESS;

}

void CreateMask(MaskType* const mask) {

 ImageType::IndexType start;
 start.Fill(0);
 ImageType::SizeType size;
 size.Fill(51);
 ImageType::RegionType region(start,size);
 mask->SetRegions(region);
 mask->Allocate();
 mask->FillBuffer(0);
 itk::ImageRegionIterator<MaskType> maskIterator(mask, region);
 //unsigned int squareSize = 8;
 unsigned int squareSize = 3;
 itk::Index<2> cornerOfSquare = Template:3,8;
 while(!maskIterator.IsAtEnd())
   {
   if(maskIterator.GetIndex()[0] > cornerOfSquare[0] &&
      maskIterator.GetIndex()[0] < cornerOfSquare[0] + squareSize &&
      maskIterator.GetIndex()[1] > cornerOfSquare[1] &&
      maskIterator.GetIndex()[1] < cornerOfSquare[1] + squareSize)
     {
     maskIterator.Set(255);
     }
   ++maskIterator;
   }

}

void CreateImage(ImageType* const 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* const 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;
   }

}

template <typename TImage> void WriteImage(const TImage* const image, const std::string& filename) {

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

}

template <typename TImage> void FillRegion(TImage* const image, const itk::ImageRegion<2>& region,

               const typename TImage::PixelType& value)

{

 itk::ImageRegionIterator<TImage> 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.