ITK/Examples/WishList/Segmentation/OtsuMultipleThresholdsCalculator

OtsuMultipleThresholdsCalculator.cxx

<source lang="cpp">

1. include "itkImage.h"
2. include "itkImageFileWriter.h"
3. include "itkOtsuThresholdImageFilter.h"
4. include "itkImageRegionIterator.h"

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

void CreateImage(ImageType::Pointer image);

int main(int, char *[]) {

 typedef itk::Image<float, 2> ImageType;
 ImageType::Pointer sumimage = ImageType::New();
 ImageType::Pointer sumimage1 = ImageType::New();
 ImageType::SizeType size;

 //THIS WORKS
 size[0]  = src_img_in.GetDimensionSize( 0 );
 size[1]  = src_img_in.GetDimensionSize( 1 );
 //
 ImageType::IndexType start;
 start.Fill(0);

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

 sumimage->SetLargestPossibleRegion( region );
 sumimage->SetBufferedRegion( region );
 sumimage->SetRequestedRegion( region );
 sumimage->Allocate();

 sumimage1->SetLargestPossibleRegion( region );
 sumimage1->SetBufferedRegion( region );
 sumimage1->SetRequestedRegion( region );
 sumimage1->Allocate();
 typedef itk::Statistics::ScalarImageToHistogramGenerator<ImageType >
 ScalarImageToHistogramGeneratorType;
 typedef
 itk::OtsuMultipleThresholdsCalculator<ScalarImageToHistogramGeneratorType::HistogramType
 > CalculatorType;
 typedef itk::BinaryThresholdImageFilter< ImageType, ImageType >
 FilterType;
 typedef itk::AddImageFilter< ImageType, ImageType ,ImageType>
 AddFilterType;

 ScalarImageToHistogramGeneratorType::Pointer
 scalarImageToHistogramGenerator =
 ScalarImageToHistogramGeneratorType::New();
 CalculatorType::Pointer calculator = CalculatorType::New();
 FilterType::Pointer filter = FilterType::New();
 AddFilterType::Pointer addFilter = AddFilterType::New();

 scalarImageToHistogramGenerator->SetNumberOfBins(n_bins);
 calculator->SetNumberOfThresholds(n_trsh);
 //THIS WORKS
 if(flag) scalarImageToHistogramGenerator->SetInput(dmtoitk2(src_img_in));
 else scalarImageToHistogramGenerator->SetInput(dmtoitk2(src_img));
 //

 calculator->SetInputHistogram(scalarImageToHistogramGenerator->GetOutput());
 filter->SetInput(dmtoitk2(src_img_in) );

 scalarImageToHistogramGenerator->Compute();
 calculator->Update();

 const CalculatorType::OutputType &thresholdVector =
 calculator->GetOutput();
 CalculatorType::OutputType::const_iterator itNum =
 thresholdVector.begin();

 //THIS WORKS
 DM::ImageCalculateMinMax( src_img_in,1, 1, &min, &max );
 //
 const float outsideValue = 0;

 float lowerThreshold = min;
 float upperThreshold;

 filter->SetOutsideValue( outsideValue );

 for(; itNum < thresholdVector.end(); itNum++)
 {

 const float insideValue = count;
 filter->SetInsideValue( insideValue );

 upperThreshold = static_cast<float>(*itNum);

 filter->SetLowerThreshold( lowerThreshold );
 filter->SetUpperThreshold( upperThreshold );
 filter->Update();

 lowerThreshold = upperThreshold;

 addFilter->SetInput1( filter->GetOutput() );
 addFilter->SetInput2(  sumimage );
 //sumimage = addFilter->GetOutput( );
 addFilter->Update();
 sumimage1 = addFilter->GetOutput() ;
 sumimage = sumimage1;

 count++;
 }
 const float insideValue = count;

 filter->SetInsideValue( count  );
 filter->SetLowerThreshold( lowerThreshold );
 filter->SetUpperThreshold( max );
 filter->Update();

 addFilter->SetInput1( filter->GetOutput() );
 addFilter->SetInput2(  sumimage );
 //sumimage = addFilter->GetOutput( );
 addFilter->Update();
 sumimage1 = addFilter->GetOutput() ;
 //THIS WORKS
 l_deriv_img_out = itktodm2( sumimage1);
 l_deriv_img_out.SetName(( std::string("Segmentated ") + name ).c_str());

 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(OtsuMultipleThresholdsCalculator)

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

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

endif()

add_executable(OtsuMultipleThresholdsCalculator MACOSX_BUNDLE OtsuMultipleThresholdsCalculator.cxx)

if( "${ITK_VERSION_MAJOR}" LESS 4 )

 target_link_libraries(OtsuMultipleThresholdsCalculator ITKReview ${ITK_LIBRARIES})

else( "${ITK_VERSION_MAJOR}" LESS 4 )

 target_link_libraries(OtsuMultipleThresholdsCalculator ${ITK_LIBRARIES})

endif( "${ITK_VERSION_MAJOR}" LESS 4 )

</syntaxhighlight>

Download and Build OtsuMultipleThresholdsCalculator

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

cd OtsuMultipleThresholdsCalculator/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:

./OtsuMultipleThresholdsCalculator

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.