ITK/Examples/WishList/Statistics/MaskedImageToHistogramFilter

The regular (non-masked) ImageToHistogramFilter has some problems, so no sense in trying this until those are resolved.

MaskedImageToHistogramFilter.cxx

<source lang="cpp">

1. include "itkMaskedImageToHistogramFilter.h"
2. include "itkImage.h"
3. include "itkImageFileWriter.h"
4. include "itkRGBPixel.h"
5. include "itkImageRegionIteratorWithIndex.h"
6. include "itkImageRegionIterator.h"
7. include "itkRescaleIntensityImageFilter.h"

typedef itk::RGBPixel<unsigned char> RGBPixelType; typedef itk::Image< RGBPixelType, 2> RGBImageType;

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

static void CreateImage(RGBImageType::Pointer image); static void CreateHalfMask(itk::ImageRegion<2>, UnsignedCharImageType::Pointer mask);

int main(int, char *[]) {

 const unsigned int MeasurementVectorSize = 3; // RGB

 RGBImageType::Pointer image = RGBImageType::New();
 CreateImage(image);

 UnsignedCharImageType::Pointer mask = UnsignedCharImageType::New();
 CreateHalfMask(image->GetLargestPossibleRegion(), mask);
 
 typedef itk::Statistics::MaskedImageToHistogramFilter< RGBImageType, UnsignedCharImageType >   HistogramFilterType;
 typedef HistogramFilterType::HistogramMeasurementVectorType             HistogramMeasurementVectorType;
 typedef HistogramFilterType::HistogramSizeType                          HistogramSizeType;
 typedef HistogramFilterType::HistogramType                              HistogramType;

 HistogramFilterType::Pointer histogramFilter = HistogramFilterType::New();
 histogramFilter->SetInput(image);
 histogramFilter->SetMaskImage(mask);
 histogramFilter->SetAutoMinimumMaximum(true);

 HistogramSizeType histogramSize( MeasurementVectorSize );

 histogramSize[0] = 4;  // number of bins for the Red   channel
 histogramSize[1] = 4;  // number of bins for the Green channel
 histogramSize[2] = 4;  // number of bins for the Blue  channel

 histogramFilter->SetHistogramSize(histogramSize);
 histogramFilter->SetMarginalScale(10); // Required (could this be set in the filter?)
 histogramFilter->Update();

 const HistogramType * histogram = histogramFilter->GetOutput();

 HistogramType::ConstIterator histogramIterator = histogram->Begin();

 //std::string filename = "/home/doriad/histogram.txt";
 //std::ofstream fout(filename.c_str());

 while( histogramIterator  != histogram->End() )
   {
   //std::cout << "Index = " << histogramIterator.GetMeasurementVector() << "Frequency = " << histogramIterator.GetFrequency() << std::endl;
   //std::cout << "Index = " << histogramIterator.GetIndex() << "Frequency = " << histogramIterator.GetFrequency() << std::endl;
   //fout << "Index = " << histogram->GetIndex(histogramItr.GetMeasurementVector()) << "Frequency = " << histogramItr.GetFrequency() << std::endl;
   ++histogramIterator ;
   }
 //fout.close();

 HistogramType::MeasurementVectorType mv(3);
 mv[0] = 255;
 mv[1] = 0;
 mv[2] = 0;
 std::cout << "Frequency = " << histogram->GetFrequency(histogram->GetIndex(mv)) << std::endl;
 return EXIT_SUCCESS;

}

void CreateImage(RGBImageType::Pointer image) {

 // Create a black image with a red square and a green square.
 // This should produce a histogram with very strong spikes.
 RGBImageType::SizeType   size;
 size[0] = 3;
 size[1] = 3;

 RGBImageType::IndexType  start;
 start[0] = 0;
 start[1] = 0;

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

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

 itk::ImageRegionIteratorWithIndex< RGBImageType > iterator( image, image->GetLargestPossibleRegion() );
 iterator.GoToBegin();

 RGBPixelType redPixel;
 redPixel.SetRed(255);
 redPixel.SetGreen(0);
 redPixel.SetBlue(0);

 RGBPixelType blackPixel;
 blackPixel.SetRed(0);
 blackPixel.SetGreen(0);
 blackPixel.SetBlue(0);

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

 while(!imageIterator.IsAtEnd())
   {
   imageIterator.Set(blackPixel);
   ++imageIterator;
   }

 RGBImageType::IndexType index;
 index[0] = 0; index[1] = 0;
 image->SetPixel(index, redPixel);

 index[0] = 1; index[1] = 0;
 image->SetPixel(index, redPixel);

}

void CreateHalfMask(itk::ImageRegion<2> region, UnsignedCharImageType::Pointer mask) {

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

 itk::Size<2> regionSize = region.GetSize();

 itk::ImageRegionIterator<UnsignedCharImageType> imageIterator(mask,region);

 // Make the left half of the mask white and the right half black
 while(!imageIterator.IsAtEnd())
 {
   if(imageIterator.GetIndex()[0] > regionSize[0] / 2)
       {
       imageIterator.Set(0);
       }
     else
       {
       imageIterator.Set(1);
       }

   ++imageIterator;
 }

 typedef itk::RescaleIntensityImageFilter< UnsignedCharImageType, UnsignedCharImageType > RescaleFilterType;
 RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
 rescaleFilter->SetInput(mask);
 rescaleFilter->Update();

 typedef  itk::ImageFileWriter< UnsignedCharImageType  > WriterType;
 WriterType::Pointer writer = WriterType::New();
 writer->SetFileName("mask.png");
 writer->SetInput(rescaleFilter->GetOutput());
 writer->Update();

}

</source>

CMakeLists.txt

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

project(MaskedImageToHistogramFilter)

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

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

endif()

add_executable(MaskedImageToHistogramFilter MACOSX_BUNDLE MaskedImageToHistogramFilter.cxx)

if( "${ITK_VERSION_MAJOR}" LESS 4 )

 target_link_libraries(MaskedImageToHistogramFilter ITKReview ${ITK_LIBRARIES})

else( "${ITK_VERSION_MAJOR}" LESS 4 )

 target_link_libraries(MaskedImageToHistogramFilter ${ITK_LIBRARIES})

endif( "${ITK_VERSION_MAJOR}" LESS 4 )

</syntaxhighlight>

Download and Build MaskedImageToHistogramFilter

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

cd MaskedImageToHistogramFilter/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:

./MaskedImageToHistogramFilter

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.