ITK  5.0.0
Insight Segmentation and Registration Toolkit
Examples/Filtering/OtsuMultipleThresholdImageFilter.cxx
/*=========================================================================
*
* Copyright Insight Software Consortium
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
// Software Guide : BeginCommandLineArgs
// INPUTS: {BrainProtonDensitySlice.png}
// ARGUMENTS: OtsuMultipleThresholdsOutput png 4
// Software Guide : EndCommandLineArgs
// Software Guide : BeginLatex
//
// This example illustrates how to use the \doxygen{OtsuMultipleThresholdsCalculator}.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
#include "itkImage.h"
#include <iomanip>
#include <cstdio>
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;
}
//Convenience type alias
using InputPixelType = unsigned short;
using OutputPixelType = unsigned char;
using InputImageType = itk::Image< InputPixelType, 2 >;
using OutputImageType = itk::Image< OutputPixelType, 2 >;
// Software Guide : BeginLatex
//
// \code{OtsuMultipleThresholdsCalculator} calculates thresholds for a given
// histogram so as to maximize the between-class variance. We use
// \code{ScalarImageToHistogramGenerator} to generate histograms. The histogram
// type defined by the generator is then used to instantiate the type of the
// Otsu threshold calculator.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using ScalarImageToHistogramGeneratorType =
using HistogramType = ScalarImageToHistogramGeneratorType::HistogramType;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Once thresholds are computed we will use \code{BinaryThresholdImageFilter}
// to segment the input image.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using FilterType = itk::BinaryThresholdImageFilter<
InputImageType, OutputImageType >;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Create a histogram generator and calculator using the standard
// \code{New()} method.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
ScalarImageToHistogramGeneratorType::Pointer scalarImageToHistogramGenerator
= ScalarImageToHistogramGeneratorType::New();
CalculatorType::Pointer calculator = CalculatorType::New();
FilterType::Pointer filter = FilterType::New();
// Software Guide : EndCodeSnippet
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
// Software Guide : BeginLatex
//
// Set the following properties for the histogram generator and the
// calculators, in this case grabbing the number of thresholds from
// the command line.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
scalarImageToHistogramGenerator->SetNumberOfBins( 128 );
calculator->SetNumberOfThresholds( std::stoi( argv[4] ) );
// Software Guide : EndCodeSnippet
calculator->SetReturnBinMidpoint( true ); //regression test requires this
constexpr OutputPixelType outsideValue = 0;
constexpr OutputPixelType insideValue = 255;
filter->SetOutsideValue( outsideValue );
filter->SetInsideValue( insideValue );
//Connect Pipeline
reader->SetFileName( argv[1] );
// Software Guide : BeginLatex
//
// The pipeline will look as follows:
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
scalarImageToHistogramGenerator->SetInput( reader->GetOutput() );
calculator->SetInputHistogram(
scalarImageToHistogramGenerator->GetOutput() );
filter->SetInput( reader->GetOutput() );
writer->SetInput( filter->GetOutput() );
// Software Guide : EndCodeSnippet
//Invoke pipeline
try
{
reader->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown while reading image" << excp << std::endl;
}
scalarImageToHistogramGenerator->Compute();
try
{
calculator->Compute();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << excp << std::endl;
}
// Software Guide : BeginLatex
//
// Here we obtain a \code{const} reference to the thresholds by calling
// the \code{GetOutput()} method.
// \index{itk::OtsuMultipleThresholdsCalculator!GetOutput()}
//
// Software Guide : EndLatex
//Get Thresholds
// Software Guide : BeginCodeSnippet
const CalculatorType::OutputType &thresholdVector = calculator->GetOutput();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We now iterate through \code{thresholdVector}, printing each value to the
// console and writing an image thresholded with adjacent values from the
// container. (In the edge cases, the minimum and maximum values of the
// \code{InternalPixelType} are used).
//
// Software Guide : EndLatex
std::string outputFileBase = argv[2];
InputPixelType lowerThreshold = itk::NumericTraits<InputPixelType>::min();
InputPixelType upperThreshold;
// Software Guide : BeginCodeSnippet
for( auto itNum = thresholdVector.begin();
itNum != thresholdVector.end();
++itNum )
{
std::cout << "OtsuThreshold["
<< (int)(itNum - thresholdVector.begin())
<< "] = "
<< static_cast<itk::NumericTraits<
CalculatorType::MeasurementType>::PrintType>(*itNum)
<< std::endl;
// Software Guide : EndCodeSnippet
upperThreshold = static_cast<InputPixelType>(*itNum);
filter->SetLowerThreshold( lowerThreshold );
filter->SetUpperThreshold( upperThreshold );
lowerThreshold = upperThreshold;
std::ostringstream outputFilename;
outputFilename << outputFileBase
<< std::setfill('0') << std::setw(3) << (itNum - thresholdVector.begin())
<< "."
<< argv[3];
writer->SetFileName( outputFilename.str() );
try
{
writer->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << excp << std::endl;
}
}
// Software Guide : BeginLatex
//
// Also write out the image thresholded between the upper threshold and
// the max intensity.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
upperThreshold = itk::NumericTraits<InputPixelType>::max();
filter->SetLowerThreshold( lowerThreshold );
filter->SetUpperThreshold( upperThreshold );
// Software Guide : EndCodeSnippet
std::ostringstream outputFilename2;
outputFilename2 << outputFileBase
<< std::setfill('0') << std::setw(3) << thresholdVector.size()
<< "."
<< argv[3];
writer->SetFileName( outputFilename2.str() );
try
{
writer->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << excp << std::endl;
}
return EXIT_SUCCESS;
}