ITK  5.2.0
Insight Toolkit
Examples/Filtering/OtsuMultipleThresholdImageFilter.cxx
/*=========================================================================
*
* Copyright NumFOCUS
*
* 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 =
// 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 (const itk::ExceptionObject & excp)
{
std::cerr << "Exception thrown while reading image" << excp << std::endl;
}
scalarImageToHistogramGenerator->Compute();
try
{
calculator->Compute();
}
catch (const 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<
*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 (const 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
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 (const itk::ExceptionObject & excp)
{
std::cerr << "Exception thrown " << excp << std::endl;
}
return EXIT_SUCCESS;
}
itk::Statistics::ScalarImageToHistogramGenerator
TODO.
Definition: itkScalarImageToHistogramGenerator.h:37
itk::BinaryThresholdImageFilter
Binarize an input image by thresholding.
Definition: itkBinaryThresholdImageFilter.h:139
itk::NumericTraits::min
static constexpr T min(const T &)
Definition: itkNumericTraits.h:172
itkImageFileReader.h
itkImage.h
itkOtsuMultipleThresholdsCalculator.h
itkScalarImageToHistogramGenerator.h
itk::ImageFileReader
Data source that reads image data from a single file.
Definition: itkImageFileReader.h:75
itk::ImageFileWriter
Writes image data to a single file.
Definition: itkImageFileWriter.h:87
itk::NumericTraits::PrintType
T PrintType
Definition: itkNumericTraits.h:68
itkImageFileWriter.h
itk::NumericTraits::max
static constexpr T max(const T &)
Definition: itkNumericTraits.h:167
itkNumericTraits.h
itkBinaryThresholdImageFilter.h
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:86
itk::OtsuMultipleThresholdsCalculator
Computes Otsu's multiple thresholds for a histogram.
Definition: itkOtsuMultipleThresholdsCalculator.h:50