ITK  5.2.0
Insight Toolkit
Examples/Segmentation/WatershedSegmentation1.cxx
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* Copyright NumFOCUS
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* Licensed under the Apache License, Version 2.0 (the "License");
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// Software Guide : BeginCommandLineArgs
// INPUTS: {VisibleWomanEyeSlice.png}
// OUTPUTS: {WatershedSegmentation1Output1.png}
// ARGUMENTS: 2 10 0 0.05 1
// Software Guide : EndCommandLineArgs
// Software Guide : BeginCommandLineArgs
// INPUTS: {VisibleWomanEyeSlice.png}
// OUTPUTS: {WatershedSegmentation1Output2.png}
// ARGUMENTS: 2 10 0.001 0.15 0
// Software Guide : EndCommandLineArgs
// Software Guide : BeginLatex
//
// The following example illustrates how to preprocess and segment images
// using the \doxygen{WatershedImageFilter}. Note that the care with which
// the data are preprocessed will greatly affect the quality of your result.
// Typically, the best results are obtained by preprocessing the original
// image with an edge-preserving diffusion filter, such as one of the
// anisotropic diffusion filters, or the bilateral image filter. As
// noted in Section~\ref{sec:AboutWatersheds}, the height function used as
// input should be created such that higher positive values correspond to
// object boundaries. A suitable height function for many applications can
// be generated as the gradient magnitude of the image to be segmented.
//
// The \doxygen{VectorGradientMagnitudeAnisotropicDiffusionImageFilter} class
// is used to smooth the image and the
// \doxygen{VectorGradientMagnitudeImageFilter} is used to generate the
// height function. We begin by including all preprocessing filter header
// files and the header file for the WatershedImageFilter. We
// use the vector versions of these filters because the input dataset is a
// color image.
//
//
// Software Guide : EndLatex
#include <iostream>
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
int
main(int argc, char * argv[])
{
if (argc < 8)
{
std::cerr << "Missing Parameters " << std::endl;
std::cerr << "Usage: " << argv[0];
std::cerr
<< " inputImage outputImage conductanceTerm diffusionIterations "
"lowerThreshold outputScaleLevel gradientMode "
<< std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// We now declare the image and pixel types to use for instantiation of the
// filters. All of these filters expect real-valued pixel types in order to
// work properly. The preprocessing stages are applied directly to the
// vector-valued data and the segmentation uses floating point
// scalar data. Images are converted from RGB pixel type to
// numerical vector type using \doxygen{CastImageFilter}.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using RGBPixelType = itk::RGBPixel<unsigned char>;
using RGBImageType = itk::Image<RGBPixelType, 2>;
using VectorPixelType = itk::Vector<float, 3>;
using VectorImageType = itk::Image<VectorPixelType, 2>;
using LabeledImageType = itk::Image<itk::IdentifierType, 2>;
using ScalarImageType = itk::Image<float, 2>;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The various image processing filters are declared using the types created
// above and eventually used in the pipeline.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using FileReaderType = itk::ImageFileReader<RGBImageType>;
using DiffusionFilterType =
VectorImageType>;
using GradientMagnitudeFilterType =
using WatershedFilterType = itk::WatershedImageFilter<ScalarImageType>;
// Software Guide : EndCodeSnippet
using FileWriterType = itk::ImageFileWriter<RGBImageType>;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetFileName(argv[1]);
CastFilterType::Pointer caster = CastFilterType::New();
// Software Guide : BeginLatex
//
// Next we instantiate the filters and set their parameters. The first
// step in the image processing pipeline is diffusion of the color input
// image using an anisotropic diffusion filter. For this class of filters,
// the CFL condition requires that the time step be no more than 0.25 for
// two-dimensional images, and no more than 0.125 for three-dimensional
// images. The number of iterations and the conductance term will be taken
// from the command line. See
// Section~\ref{sec:EdgePreservingSmoothingFilters} for more information on
// the ITK anisotropic diffusion filters.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
DiffusionFilterType::Pointer diffusion = DiffusionFilterType::New();
diffusion->SetNumberOfIterations(std::stoi(argv[4]));
diffusion->SetConductanceParameter(std::stod(argv[3]));
diffusion->SetTimeStep(0.125);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The ITK gradient magnitude filter for vector-valued images can optionally
// take several parameters. Here we allow only enabling or disabling
// of principal component analysis.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
GradientMagnitudeFilterType::Pointer gradient =
GradientMagnitudeFilterType::New();
gradient->SetUsePrincipleComponents(std::stoi(argv[7]));
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Finally we set up the watershed filter. There are two parameters.
// \code{Level} controls watershed depth, and \code{Threshold} controls the
// lower thresholding of the input. Both parameters are set as a
// percentage (0.0 - 1.0) of the maximum depth in the input image.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
WatershedFilterType::Pointer watershed = WatershedFilterType::New();
watershed->SetLevel(std::stod(argv[6]));
watershed->SetThreshold(std::stod(argv[5]));
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The output of WatershedImageFilter is an image of unsigned long integer
// labels, where a label denotes membership of a pixel in a particular
// segmented region. This format is not practical for visualization, so
// for the purposes of this example, we will convert it to RGB pixels. RGB
// images have the advantage that they can be saved as a simple png file
// and viewed using any standard image viewer software. The
// \subdoxygen{Functor}{ScalarToRGBPixelFunctor} class is a special
// function object designed to hash a scalar value into an
// \doxygen{RGBPixel}. Plugging this functor into the
// \doxygen{UnaryFunctorImageFilter} creates an image filter which
// converts scalar images to RGB images.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using ColormapFunctorType =
using ColormapFilterType =
itk::UnaryFunctorImageFilter<LabeledImageType,
RGBImageType,
ColormapFunctorType>;
ColormapFilterType::Pointer colormapper = ColormapFilterType::New();
// Software Guide : EndCodeSnippet
FileWriterType::Pointer writer = FileWriterType::New();
writer->SetFileName(argv[2]);
// Software Guide : BeginLatex
//
// The filters are connected into a single pipeline, with readers and
// writers at each end.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
caster->SetInput(reader->GetOutput());
diffusion->SetInput(caster->GetOutput());
gradient->SetInput(diffusion->GetOutput());
watershed->SetInput(gradient->GetOutput());
colormapper->SetInput(watershed->GetOutput());
writer->SetInput(colormapper->GetOutput());
// Software Guide : EndCodeSnippet
try
{
writer->Update();
}
catch (const itk::ExceptionObject & e)
{
std::cerr << e << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
//
// Software Guide : BeginLatex
//
// \begin{figure} \center
// \includegraphics[width=0.32\textwidth]{VisibleWomanEyeSlice}
// \includegraphics[width=0.32\textwidth]{WatershedSegmentation1Output1}
// \includegraphics[width=0.32\textwidth]{WatershedSegmentation1Output2}
// \itkcaption[Watershed segmentation output]{Segmented section of Visible
// Human female head and neck cryosection data. At left is the original
// image. The image in the middle was generated with parameters: conductance
// = 2.0, iterations = 10, threshold = 0.0, level = 0.05, principal components
// = on. The image on the right was generated with parameters: conductance
// = 2.0, iterations = 10, threshold = 0.001, level = 0.15, principal
// components = off. } \label{fig:outputWatersheds} \end{figure}
//
//
// Tuning the filter parameters for any particular application is a process
// of trial and error. The \emph{threshold} parameter can be used to great
// effect in controlling oversegmentation of the image. Raising the
// threshold will generally reduce computation time and produce output with
// fewer and larger regions. The trick in tuning parameters is to consider
// the scale level of the objects that you are trying to segment in the
// image. The best time/quality trade-off will be achieved when the image is
// smoothed and thresholded to eliminate features just below the desired
// scale.
//
// Figure~\ref{fig:outputWatersheds} shows output from the example code. The
// input image is taken from the Visible Human female data around the right
// eye. The images on the right are colorized watershed segmentations with
// parameters set to capture objects such as the optic nerve and
// lateral rectus muscles, which can be seen just above and to the left and
// right of the eyeball. Note that a critical difference between the two
// segmentations is the mode of the gradient magnitude calculation.
//
// A note on the computational complexity of the watershed algorithm is
// warranted. Most of the complexity of the ITK implementation lies in
// generating the hierarchy. Processing times for this stage are non-linear
// with respect to the number of catchment basins in the initial segmentation.
// This means that the amount of information contained in an image is more
// significant than the number of pixels in the image. A very large, but very
// flat input take less time to segment than a very small, but very detailed
// input.
//
// Software Guide : EndLatex
itk::CastImageFilter
Casts input pixels to output pixel type.
Definition: itkCastImageFilter.h:104
itk::RGBPixel
Represent Red, Green and Blue components for color images.
Definition: itkRGBPixel.h:58
itk::Functor::ScalarToRGBPixelFunctor
A Function object which maps a scalar value into an RGB pixel value.
Definition: itkScalarToRGBPixelFunctor.h:44
itk::VectorGradientMagnitudeImageFilter
Computes a scalar, gradient magnitude image from a multiple channel (pixels are vectors) input.
Definition: itkVectorGradientMagnitudeImageFilter.h:138
itkVectorGradientMagnitudeImageFilter.h
itk::UnaryFunctorImageFilter
Implements pixel-wise generic operation on one image.
Definition: itkUnaryFunctorImageFilter.h:50
itkScalarToRGBPixelFunctor.h
itk::Vector
A templated class holding a n-Dimensional vector.
Definition: itkVector.h:62
itkImageFileReader.h
itkVectorGradientAnisotropicDiffusionImageFilter.h
itkCastImageFilter.h
itk::WatershedImageFilter
A low-level image analysis algorithm that automatically produces a hierarchy of segmented,...
Definition: itkWatershedImageFilter.h:149
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::VectorGradientAnisotropicDiffusionImageFilter
Definition: itkVectorGradientAnisotropicDiffusionImageFilter.h:61
itkImageFileWriter.h
itkWatershedImageFilter.h
itk::Math::e
static constexpr double e
Definition: itkMath.h:54
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:86