ITK/Examples/ImageProcessing/LabelGeometryImageFilter

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ITK Examples Baseline ImageProcessing TestLabelGeometryImageFilter.png

NOTE: Requires a QuickView as of April 8, 2015. Otherwise, comment out InterpolateOff() statements.

LabelGeometryImageFilter.cxx

<source lang="cpp">

  1. include "itkImage.h"
  2. include "itkImageFileWriter.h"
  3. include "itkImageRegionIterator.h"
  4. include "itkImageFileReader.h"
  5. include "itkLabelGeometryImageFilter.h"
  6. include "itkLabelToRGBImageFilter.h"
  1. include "QuickView.h"
  1. include <sstream>

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

static void CreateIntensityImage(ImageType::Pointer image); static void CreateLabelImage(ImageType::Pointer image);

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

 ImageType::Pointer labelImage = ImageType::New();
 ImageType::Pointer intensityImage = ImageType::New();
 int label = 1;

 if (argc < 2)
   {
   // Create a label image that is 0 in the background and where the
   // objects are labeled
   CreateLabelImage(labelImage);
   labelImage->Print(std::cout);
   // Create an intensity image.  Some LabelGeometry features (such as
   // weighted centroid and integrated intensity) depend on an
   // intensity image.
   CreateIntensityImage(intensityImage);
   }
 else if (argc > 3)
   {
   typedef itk::ImageFileReader< ImageType  > ImageReaderType;
   ImageReaderType::Pointer labelReader =
     ImageReaderType::New();
   labelReader->SetFileName(argv[1]);
   labelReader->Update();

   labelImage = labelReader->GetOutput();

   ImageReaderType::Pointer intensityReader =
     ImageReaderType::New();
   intensityReader->SetFileName(argv[2]);
   intensityReader->Update();

   intensityImage = intensityReader->GetOutput();

   label = atoi(argv[3]);
   }

 // NOTE: As of April 8, 2015 the filter does not work with non-zero
 // origins
 double origin[2] = {0.0, 0.0};
 labelImage->SetOrigin(origin);
 intensityImage->SetOrigin(origin);

 typedef itk::LabelGeometryImageFilter< ImageType > LabelGeometryImageFilterType;
 LabelGeometryImageFilterType::Pointer labelGeometryImageFilter = LabelGeometryImageFilterType::New();
 labelGeometryImageFilter->SetInput( labelImage );
 labelGeometryImageFilter->SetIntensityInput( intensityImage );

 // These generate optional outputs.
 labelGeometryImageFilter->CalculatePixelIndicesOn();
 labelGeometryImageFilter->CalculateOrientedBoundingBoxOn();
 labelGeometryImageFilter->CalculateOrientedLabelRegionsOn();
 labelGeometryImageFilter->CalculateOrientedIntensityRegionsOn();
 
 labelGeometryImageFilter->Update();
 LabelGeometryImageFilterType::LabelsType allLabels =
   labelGeometryImageFilter->GetLabels();
 
 typedef itk::LabelToRGBImageFilter<ImageType, RGBImageType> RGBFilterType;
 RGBFilterType::Pointer rgbLabelImage =
   RGBFilterType::New();
 rgbLabelImage->SetInput(labelImage);

 typedef itk::LabelToRGBImageFilter<ImageType, RGBImageType> RGBFilterType;
 RGBFilterType::Pointer rgbOrientedImage =
   RGBFilterType::New();
 rgbOrientedImage->SetInput(labelGeometryImageFilter->GetOrientedLabelImage(allLabels[label]));

 QuickView viewer;
 viewer.ShareCameraOff();
 viewer.InterpolateOff();

 viewer.AddImage(
   rgbLabelImage->GetOutput(),
   true,
   argc > 3 ? itksys::SystemTools::GetFilenameName(argv[1]) : "Generated label image");  
 viewer.AddImage(
   intensityImage.GetPointer(),
   true,
   argc > 3 ? itksys::SystemTools::GetFilenameName(argv[2]) : "Generated intensity image");

 std::stringstream desc;
 desc << "Oriented Label: " << allLabels[label];
 viewer.AddImage(
   rgbOrientedImage->GetOutput(),
   true,
   desc.str());  

 std::stringstream desc2;
 desc2 << "Oriented Intensity: " << allLabels[label];
 viewer.AddImage(
   labelGeometryImageFilter->GetOrientedIntensityImage(allLabels[label]),
   true,
   desc2.str());  
 viewer.Visualize();

 LabelGeometryImageFilterType::LabelsType::iterator allLabelsIt;
 std::cout << "Number of labels: "
           << labelGeometryImageFilter->GetNumberOfLabels() << std::endl;
 std::cout << std::endl;

 for( allLabelsIt = allLabels.begin(); allLabelsIt != allLabels.end(); allLabelsIt++ )
   {
   LabelGeometryImageFilterType::LabelPixelType labelValue = *allLabelsIt;
   std::cout << "\tLabel: "
             << (int)labelValue << std::endl;
   std::cout << "\tVolume: "
             << labelGeometryImageFilter->GetVolume(labelValue) << std::endl;
   std::cout << "\tIntegrated Intensity: "
             << labelGeometryImageFilter->GetIntegratedIntensity(labelValue) << std::endl;
   std::cout << "\tCentroid: "
             << labelGeometryImageFilter->GetCentroid(labelValue) << std::endl;
   std::cout << "\tWeighted Centroid: "
             << labelGeometryImageFilter->GetWeightedCentroid(labelValue) << std::endl;
   std::cout << "\tAxes Length: "
             << labelGeometryImageFilter->GetAxesLength(labelValue) << std::endl;
   std::cout << "\tMajorAxisLength: "
             << labelGeometryImageFilter->GetMajorAxisLength(labelValue) << std::endl;
   std::cout << "\tMinorAxisLength: "
             << labelGeometryImageFilter->GetMinorAxisLength(labelValue) << std::endl;
   std::cout << "\tEccentricity: "
             << labelGeometryImageFilter->GetEccentricity(labelValue) << std::endl;
   std::cout << "\tElongation: "
             << labelGeometryImageFilter->GetElongation(labelValue) << std::endl;
   std::cout << "\tOrientation: "
             << labelGeometryImageFilter->GetOrientation(labelValue) << std::endl;
   std::cout << "\tBounding box: "
             << labelGeometryImageFilter->GetBoundingBox(labelValue) << std::endl;
   
   std::cout << std::endl << std::endl;
   }

 return EXIT_SUCCESS;

}

void CreateIntensityImage(ImageType::Pointer image) { 

 // Create a random image.
 ImageType::IndexType start;
 start.Fill(0);

 ImageType::SizeType size;
 size.Fill(20);

 ImageType::RegionType region;
 region.SetSize(size);
 region.SetIndex(start);
 image->SetRegions(region);
 image->Allocate();

 itk::ImageRegionIterator<ImageType> imageIterator(image,image->GetLargestPossibleRegion());
 // Make a random image
 // Create an unchanging seed.
 srand(1);
 while(!imageIterator.IsAtEnd())
   {
   int randomNumber = rand() % 255;
   imageIterator.Set( randomNumber );
   ++imageIterator;
   }

}

void CreateLabelImage(ImageType::Pointer image) { 

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

 ImageType::SizeType size;
 size.Fill(20);

 ImageType::RegionType region;
 region.SetSize(size);
 region.SetIndex(start);
 image->SetRegions(region);
 image->Allocate();

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

 // Make a square
 while(!imageIterator.IsAtEnd())
   {
   if((imageIterator.GetIndex()[0] > 5 && imageIterator.GetIndex()[0] < 10) &&
     (imageIterator.GetIndex()[1] > 5 && imageIterator.GetIndex()[1] < 10) )
       {
       imageIterator.Set(85);
       }
   else if((imageIterator.GetIndex()[0] > 11 && imageIterator.GetIndex()[0] < 17) &&
     (imageIterator.GetIndex()[1] > 11 && imageIterator.GetIndex()[1] < 17) )

{ imageIterator.Set(127); } 

   else if((imageIterator.GetIndex()[0] > 11 && imageIterator.GetIndex()[0] < 17) &&
     (imageIterator.GetIndex()[1] > 1 && imageIterator.GetIndex()[1] < 5) )

{ imageIterator.Set(191); } 

   else
       {
       imageIterator.Set(0);
       }

   ++imageIterator;
   }

} </source>

CMakeLists.txt

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

project(LabelGeometryImageFilter)

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

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

endif()

add_executable(LabelGeometryImageFilter MACOSX_BUNDLE LabelGeometryImageFilter.cxx)

if( "${ITK_VERSION_MAJOR}" LESS 4 ) 

 target_link_libraries(LabelGeometryImageFilter ITKReview ${ITK_LIBRARIES})

else( "${ITK_VERSION_MAJOR}" LESS 4 ) 

 target_link_libraries(LabelGeometryImageFilter ${ITK_LIBRARIES})

endif( "${ITK_VERSION_MAJOR}" LESS 4 )

</syntaxhighlight>

Download and Build LabelGeometryImageFilter

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

cd LabelGeometryImageFilter/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: 

./LabelGeometryImageFilter

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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