ITK/Examples/Segmentation/OtsuMultipleThresholdsImageFilter

OtsuMultipleThresholdsImageFilter.cxx

<source lang="cpp">

1. include "itkImage.h"
2. include "itkOtsuMultipleThresholdsImageFilter.h"
3. include "itkImageFileReader.h"
4. include "itkImageRegionIterator.h"
5. include "itkNumericTraits.h"
6. include "itkLabelToRGBImageFilter.h"

1. include "itksys/SystemTools.hxx"
2. include <sstream>

1. include "QuickView.h"

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

static void CreateImage(ImageType::Pointer image);

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

 unsigned int numberOfThresholds = 1;
 ImageType::Pointer image;
 if( argc < 2 )
   {
   image = ImageType::New();
   CreateImage(image.GetPointer());
   }
 else
   {
   typedef itk::ImageFileReader<ImageType> ReaderType;
   ReaderType::Pointer reader =
     ReaderType::New();
   reader->SetFileName(argv[1]);
   reader->Update();
   if (argc > 2)
     {
     numberOfThresholds = atoi(argv[2]);
     }
   image = reader->GetOutput();
   }

 typedef itk::OtsuMultipleThresholdsImageFilter <ImageType, ImageType>
         FilterType;
 FilterType::Pointer otsuFilter
         = FilterType::New();
 otsuFilter->SetInput(image);
 otsuFilter->SetNumberOfThresholds(numberOfThresholds);
 otsuFilter->Update(); // To compute threshold

 typedef itk::LabelToRGBImageFilter<ImageType, RGBImageType> RGBFilterType;
 RGBFilterType::Pointer colormapImageFilter = RGBFilterType::New();
 colormapImageFilter->SetInput(otsuFilter->GetOutput());

 QuickView viewer;
 viewer.AddImage(
   image.GetPointer(),true,
   argc > 1 ? itksys::SystemTools::GetFilenameName(argv[1]) : "Generated image");

 std::stringstream desc;
 desc << "Otsu Threshold\n"
      << otsuFilter->GetNumberOfThresholds()
      << " thresholds: ";
 FilterType::ThresholdVectorType thresholds = otsuFilter->GetThresholds();
 for (unsigned int i = 0; i < thresholds.size(); i++)
   {
   desc << itk::NumericTraits<FilterType::InputPixelType>::PrintType(thresholds[i]) << " ";
   }

 viewer.AddRGBImage(
   colormapImageFilter->GetOutput(),
   true,
   desc.str());  

 viewer.Visualize();

 return EXIT_SUCCESS;

}

void CreateImage(ImageType::Pointer image) {

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

 ImageType::SizeType size;
 size.Fill(100);

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

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

 // Make the whole image white
 itk::ImageRegionIterator<ImageType> iterator(image,image->GetLargestPossibleRegion());

 /*
  //Create a square
 while(!iterator.IsAtEnd())
   {
   iterator.Set(255);
   ++iterator;
   }
 */

} </source>

CMakeLists.txt

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

project(OtsuMultipleThresholdsImageFilter)

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(OtsuMultipleThresholdsImageFilter MACOSX_BUNDLE OtsuMultipleThresholdsImageFilter.cxx) target_link_libraries(OtsuMultipleThresholdsImageFilter

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

</syntaxhighlight>

Download and Build OtsuMultipleThresholdsImageFilter

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

cd OtsuMultipleThresholdsImageFilter/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:

./OtsuMultipleThresholdsImageFilter

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.