ITK/Examples/Segmentation/WatershedImageFilter

WatershedImageFilter.cxx

<source lang="cpp">

1. include <iostream>

1. include "itkImageFileReader.h"
2. include "itkImageFileWriter.h"
3. include "itkScalarToRGBPixelFunctor.h"
4. include "itkUnaryFunctorImageFilter.h"
5. include "itkVectorCastImageFilter.h"
6. include "itkVectorGradientAnisotropicDiffusionImageFilter.h"
7. include "itkVectorMagnitudeImageFilter.h"
8. include "itkWatershedImageFilter.h"
9. include "itkRescaleIntensityImageFilter.h"
10. include "itkScalarToRGBColormapImageFilter.h"
11. include "itkGradientMagnitudeImageFilter.h"

// Run with: // ./WatershedImageFilter threshold level // e.g. // ./WatershedImageFilter 0.005 .5 // (A rule of thumb is to set the Threshold to be about 1 / 100 of the Level.)

typedef itk::Image<unsigned char, 2> UnsignedCharImageType; typedef itk::Image<float, 2> FloatImageType; typedef itk::RGBPixel<unsigned char> RGBPixelType; typedef itk::Image<RGBPixelType, 2> RGBImageType; typedef itk::Image<unsigned long, 2> LabeledImageType;

static void CreateImage(UnsignedCharImageType::Pointer image); static void PerformSegmentation(FloatImageType::Pointer image, const float threshold, const float level);

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

 // Verify arguments
 if (argc < 3 )
   {
   std::cerr << "Parameters " << std::endl;
   std::cerr << " threshold level" << std::endl;
   return 1;
   }

 // Parse arguments
 std::string strThreshold = argv[1];
 float threshold = 0.0;
 std::stringstream ssThreshold;
 ssThreshold << strThreshold;
 ssThreshold >> threshold;
 
 std::string strLevel = argv[2];
 float level = 0.0;
 std::stringstream ssLevel;
 ssLevel << strLevel;
 ssLevel >> level;
 
 // Output arguments
 std::cout << "Running with:" << std::endl
           << "Threshold: " << threshold << std::endl
           << "Level: " << level << std::endl;
 
 UnsignedCharImageType::Pointer image = UnsignedCharImageType::New();
 CreateImage(image);
 
 typedef itk::GradientMagnitudeImageFilter<
   UnsignedCharImageType, FloatImageType >  GradientMagnitudeImageFilterType;
 GradientMagnitudeImageFilterType::Pointer gradientMagnitudeImageFilter = GradientMagnitudeImageFilterType::New();
 gradientMagnitudeImageFilter->SetInput(image);
 gradientMagnitudeImageFilter->Update();

 // Custom parameters
 PerformSegmentation(gradientMagnitudeImageFilter->GetOutput(), threshold, level);
 
 // Fixed parameters
 PerformSegmentation(gradientMagnitudeImageFilter->GetOutput(), .0025, .25);
 PerformSegmentation(gradientMagnitudeImageFilter->GetOutput(), .005, .5);
 PerformSegmentation(gradientMagnitudeImageFilter->GetOutput(), .0075, .75);
 PerformSegmentation(gradientMagnitudeImageFilter->GetOutput(), .009, .9);
 
 return EXIT_SUCCESS;

}

void CreateImage(UnsignedCharImageType::Pointer image) {

 // Create a white image with 3 dark regions of different values
 
 itk::Index<2> start;
 start.Fill(0);

 itk::Size<2> size;
 size.Fill(200);

 itk::ImageRegion<2> region(start,size);
 image->SetRegions(region);
 image->Allocate();
 image->FillBuffer(255);

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

 while(!imageIterator.IsAtEnd())
   {
   if(imageIterator.GetIndex()[0] > 20 && imageIterator.GetIndex()[0] < 50 &&
      imageIterator.GetIndex()[1] > 20 && imageIterator.GetIndex()[1] < 50)
   imageIterator.Set(50);

   ++imageIterator;
   }
   
 imageIterator.GoToBegin();
 
 while(!imageIterator.IsAtEnd())
   {
   if(imageIterator.GetIndex()[0] > 60 && imageIterator.GetIndex()[0] < 80 &&
      imageIterator.GetIndex()[1] > 60 && imageIterator.GetIndex()[1] < 80)
   imageIterator.Set(100);

   ++imageIterator;
   }
   
 imageIterator.GoToBegin();
 
 while(!imageIterator.IsAtEnd())
   {
   if(imageIterator.GetIndex()[0] > 100 && imageIterator.GetIndex()[0] < 130 &&
      imageIterator.GetIndex()[1] > 100 && imageIterator.GetIndex()[1] < 130)
   imageIterator.Set(150);

   ++imageIterator;
   }
   
 typedef itk::ImageFileWriter<UnsignedCharImageType> FileWriterType;
 FileWriterType::Pointer writer = FileWriterType::New();
 writer->SetFileName("input.png");
 writer->SetInput(image);
 writer->Update();

}

void PerformSegmentation(FloatImageType::Pointer image, const float threshold, const float level) {

 typedef itk::WatershedImageFilter<FloatImageType> WatershedFilterType;
 WatershedFilterType::Pointer watershed = WatershedFilterType::New();
 watershed->SetThreshold(threshold);
 watershed->SetLevel(level);
 watershed->SetInput(image);
 watershed->Update();

 typedef itk::ScalarToRGBColormapImageFilter<LabeledImageType, RGBImageType> RGBFilterType;
 RGBFilterType::Pointer colormapImageFilter = RGBFilterType::New();
 colormapImageFilter->SetInput(watershed->GetOutput());
 colormapImageFilter->SetColormap( RGBFilterType::Jet );
 colormapImageFilter->Update();

 std::stringstream ss;
 ss << "output_" << threshold << "_" << level << ".png";
 
 typedef itk::ImageFileWriter<RGBImageType> FileWriterType;
 FileWriterType::Pointer writer = FileWriterType::New();
 writer->SetFileName(ss.str());
 writer->SetInput(colormapImageFilter->GetOutput());
 writer->Update();
   

}

</source>

CMakeLists.txt

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

project(WatershedImageFilter)

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

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

endif()

add_executable(WatershedImageFilter MACOSX_BUNDLE WatershedImageFilter.cxx)

if( "${ITK_VERSION_MAJOR}" LESS 4 )

 target_link_libraries(WatershedImageFilter ITKReview ${ITK_LIBRARIES})

else( "${ITK_VERSION_MAJOR}" LESS 4 )

 target_link_libraries(WatershedImageFilter ${ITK_LIBRARIES})

endif( "${ITK_VERSION_MAJOR}" LESS 4 )

</syntaxhighlight>

Download and Build WatershedImageFilter

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

cd WatershedImageFilter/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:

./WatershedImageFilter

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.