[Insight-users] OtsuMultipleThresholdImageFilter

[David Doria]

On Fri, Apr 8, 2011 at 10:32 AM, john smith <mkitkinsightuser at gmail.com>wrote:

> Hello,
>  I have the followin code from itk-manual to run
> OtsuMultipleThresholdImageFilter. What must I type in the command window to
> run the project?
> Thanks in advance
>
> ////////////  code//////////////
>
>
> #include "itkOtsuMultipleThresholdsCalculator.h"
>
>
> #include "itkImage.h"
> #include "itkImageFileReader.h"
> #include "itkImageFileWriter.h"
> #include "itkScalarImageToHistogramGenerator.h"
> #include "itkBinaryThresholdImageFilter.h"
> #include "itkNumericTraits.h"
>
> #include <stdio.h>
> int main( int argc, char * argv[] )
> {
>   if( argc < 5 )
>     {
>     std::cerr << "Usage: " << argv[0];
>     std::cerr << " inputImageFile outputImageFileBase ";
>     std::cerr << "  outputImageFileExtension numberOfThresholdsToCalculate
> "  << std::endl;
>     return EXIT_FAILURE;
>     }
>
>
>   typedef  unsigned short  InputPixelType;
>   typedef  unsigned char   OutputPixelType;
>
>   typedef itk::Image< InputPixelType,  3 >   InputImageType;
>   typedef itk::Image< OutputPixelType, 3 >   OutputImageType;
>
>
>   typedef itk::Statistics::ScalarImageToHistogramGenerator<
>   InputImageType >
>     ScalarImageToHistogramGeneratorType;
>
>   typedef ScalarImageToHistogramGeneratorType::HistogramType
> HistogramType;
>
>   typedef itk::OtsuMultipleThresholdsCalculator< HistogramType >
> CalculatorType;
>
>
>   typedef itk::ImageFileReader< InputImageType >  ReaderType;
>   typedef itk::ImageFileWriter< OutputImageType >  WriterType;
>
>
>   typedef itk::BinaryThresholdImageFilter<
>   InputImageType, OutputImageType >  FilterType;
>
>   ScalarImageToHistogramGeneratorType::Pointer
> scalarImageToHistogramGenerator =
>     ScalarImageToHistogramGeneratorType::New();
>
>   CalculatorType::Pointer calculator = CalculatorType::New();
>   FilterType::Pointer filter = FilterType::New();
>
>
>   ReaderType::Pointer reader = ReaderType::New();
>   WriterType::Pointer writer = WriterType::New();
>
>
>   scalarImageToHistogramGenerator->SetNumberOfBins( 128 );
>   calculator->SetNumberOfThresholds( atoi( argv[4] ) );
>
>   const OutputPixelType outsideValue = 0;
>   const OutputPixelType insideValue = 255;
>
>   filter->SetOutsideValue( outsideValue );
>   filter->SetInsideValue(  insideValue  );
>
>
>   reader->SetFileName( argv[1] );
>
>
>   scalarImageToHistogramGenerator->SetInput( reader->GetOutput() );
>   calculator->SetInputHistogram(
> scalarImageToHistogramGenerator->GetOutput() );
>   filter->SetInput( reader->GetOutput() );
>   writer->SetInput( filter->GetOutput() );
>
>   try
>     {
>     reader->Update();
>     }
>   catch( itk::ExceptionObject & excp )
>     {
>     std::cerr << "Exception thrown while reading image" << excp <<
> std::endl;
>     }
>   scalarImageToHistogramGenerator->Compute();
>
>   try
>     {
>     calculator->Update();
>     }
>   catch( itk::ExceptionObject & excp )
>     {
>     std::cerr << "Exception thrown " << excp << std::endl;
>     }
>
>
>   const CalculatorType::OutputType &thresholdVector =
> calculator->GetOutput();
>   CalculatorType::OutputType::const_iterator itNum =
> thresholdVector.begin();
>
>   std::string outputFileBase = argv[2];
>   std::string outputFile;
>
>   InputPixelType lowerThreshold = 0;
>   InputPixelType upperThreshold;
>
>   std::string format = argv[2];
>
>   char outputFilename[1000];
>   outputFile = outputFileBase + "%03d.";
>   outputFile += argv[3];   // filename extension
>
>
>   for(; itNum < thresholdVector.end(); itNum++)
>     {
>     std::cout << "OtsuThreshold["
>               << (int)(itNum - thresholdVector.begin())
>               << "] = "
>               <<
> static_cast<itk::NumericTraits<CalculatorType::MeasurementType>::PrintType>(*itNum)
>
>               << std::endl;
>
>
>     upperThreshold = static_cast<InputPixelType>(*itNum);
>
>     filter->SetLowerThreshold( lowerThreshold );
>     filter->SetUpperThreshold( upperThreshold );
>
>     lowerThreshold = upperThreshold;
>
>     sprintf (outputFilename, outputFile.c_str(), (itNum -
> thresholdVector.begin()));
>     writer->SetFileName( outputFilename );
>
>
>     try
>       {
>       writer->Update();
>       }
>     catch( itk::ExceptionObject & excp )
>       {
>       std::cerr << "Exception thrown " << excp << std::endl;
>       }
>
>     }
>
>   upperThreshold = itk::NumericTraits<InputPixelType>::max();
>   filter->SetLowerThreshold( lowerThreshold );
>   filter->SetUpperThreshold( upperThreshold );
>
>   sprintf (outputFilename, outputFile.c_str(), (thresholdVector.size() ));
>   writer->SetFileName( outputFilename );
>
>   try
>     {
>     writer->Update();
>     }
>   catch( itk::ExceptionObject & excp )
>     {
>     std::cerr << "Exception thrown " << excp << std::endl;
>     }
>
>
>   return EXIT_SUCCESS;
> }
>
>
At the top of the example there is an explanation:

//    INPUTS: {BrainProtonDensitySlice.png}
//    OtsuMultipleThresholdsOutput png 4

I would guess that this would translate to :

./ThisProgram BrainProtonDensitySlice.png OtsuMultipleThresholdsOutput png
4

I'm not sure why INPUTS{} is in brackets, etc.

David
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