ITK  5.1.0
Insight Toolkit
Examples/Segmentation/ConfidenceConnected.cxx
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* Licensed under the Apache License, Version 2.0 (the "License");
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// Software Guide : BeginCommandLineArgs
// INPUTS: {BrainProtonDensitySlice.png}
// OUTPUTS: {ConfidenceConnectedOutput1.png}
// ARGUMENTS: 60 116
// Software Guide : EndCommandLineArgs
// Software Guide : BeginCommandLineArgs
// INPUTS: {BrainProtonDensitySlice.png}
// OUTPUTS: {ConfidenceConnectedOutput2.png}
// ARGUMENTS: 81 112
// Software Guide : EndCommandLineArgs
// Software Guide : BeginCommandLineArgs
// INPUTS: {BrainProtonDensitySlice.png}
// OUTPUTS: {ConfidenceConnectedOutput3.png}
// ARGUMENTS: 107 69
// Software Guide : EndCommandLineArgs
// Software Guide : BeginLatex
//
// \index{itk::FloodFillIterator!In Region Growing}
// \index{itk::ConfidenceConnectedImageFilter}
// \index{itk::ConfidenceConnectedImageFilter!header}
//
// The following example illustrates the use of the
// \doxygen{ConfidenceConnectedImageFilter}. The criterion used by the
// ConfidenceConnectedImageFilter is based on simple statistics of the
// current region. First, the algorithm computes the mean and standard
// deviation of intensity values for all the pixels currently included in the
// region. A user-provided factor is used to multiply the standard deviation
// and define a range around the mean. Neighbor pixels whose intensity values
// fall inside the range are accepted and included in the region. When no
// more neighbor pixels are found that satisfy the criterion, the algorithm
// is considered to have finished its first iteration. At that point, the
// mean and standard deviation of the intensity levels are recomputed using
// all the pixels currently included in the region. This mean and standard
// deviation defines a new intensity range that is used to visit current
// region neighbors and evaluate whether their intensity falls inside the
// range. This iterative process is repeated until no more pixels are added
// or the maximum number of iterations is reached. The following equation
// illustrates the inclusion criterion used by this filter,
//
// \begin{equation}
// I(\mathbf{X}) \in [ m - f \sigma , m + f \sigma ]
// \end{equation}
//
// where $m$ and $\sigma$ are the mean and standard deviation of the region
// intensities, $f$ is a factor defined by the user, $I()$ is the image and
// $\mathbf{X}$ is the position of the particular neighbor pixel being
// considered for inclusion in the region.
//
// Let's look at the minimal code required to use this algorithm. First, the
// following header defining the \doxygen{ConfidenceConnectedImageFilter} class
// must be included.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Noise present in the image can reduce the capacity of this filter to grow
// large regions. When faced with noisy images, it is usually convenient to
// pre-process the image by using an edge-preserving smoothing filter. Any of
// the filters discussed in Section~\ref{sec:EdgePreservingSmoothingFilters}
// can be used to this end. In this particular example we use the
// \doxygen{CurvatureFlowImageFilter}, hence we need to include its header
// file.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
int
main(int argc, char * argv[])
{
if (argc < 5)
{
std::cerr << "Missing Parameters " << std::endl;
std::cerr << "Usage: " << argv[0];
std::cerr << " inputImage outputImage seedX seedY " << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// We now define the image type using a pixel type and a particular
// dimension. In this case the \code{float} type is used for the pixels due
// to the requirements of the smoothing filter.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using InternalPixelType = float;
constexpr unsigned int Dimension = 2;
using InternalImageType = itk::Image<InternalPixelType, Dimension>;
// Software Guide : EndCodeSnippet
using OutputPixelType = unsigned char;
using OutputImageType = itk::Image<OutputPixelType, Dimension>;
CastingFilterType::Pointer caster = CastingFilterType::New();
// We instantiate reader and writer types
//
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
reader->SetFileName(argv[1]);
writer->SetFileName(argv[2]);
// Software Guide : BeginLatex
//
// The smoothing filter type is instantiated using the image type as
// a template parameter.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using CurvatureFlowImageFilterType =
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Next the filter is created by invoking the \code{New()} method and
// assigning the result to a \doxygen{SmartPointer}.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
CurvatureFlowImageFilterType::Pointer smoothing = CurvatureFlowImageFilterType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We now declare the type of the region growing filter. In this case it is
// the \code{ConfidenceConnectedImageFilter}.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using ConnectedFilterType =
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Then, we construct one filter of this class using the \code{New()}
// method.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
ConnectedFilterType::Pointer confidenceConnected = ConnectedFilterType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Now it is time to create a simple, linear pipeline. A file reader is
// added at the beginning of the pipeline and a cast filter and writer are
// added at the end. The cast filter is required here to convert
// \code{float} pixel types to integer types since only a few image file
// formats support \code{float} types.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
smoothing->SetInput(reader->GetOutput());
confidenceConnected->SetInput(smoothing->GetOutput());
caster->SetInput(confidenceConnected->GetOutput());
writer->SetInput(caster->GetOutput());
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// \code{CurvatureFlowImageFilter} requires two parameters. The
// following are typical values for $2D$ images. However they may have to
// be adjusted depending on the amount of noise present in the input
// image.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
smoothing->SetNumberOfIterations(5);
smoothing->SetTimeStep(0.125);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// \code{ConfidenceConnectedImageFilter} also requires two parameters.
// First, the factor $f$ defines how large the range of
// intensities will be. Small values of the multiplier will restrict the
// inclusion of pixels to those having very similar intensities to those
// in the current region. Larger values of the multiplier will relax the
// accepting condition and will result in more generous growth of the
// region. Values that are too large will cause the region to grow into
// neighboring regions which may belong to separate anatomical
// structures. This is not desirable behavior.
//
// \index{itk::ConfidenceConnectedImageFilter!SetMultiplier()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
confidenceConnected->SetMultiplier(2.5);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The number of iterations is specified based on the homogeneity of the
// intensities of the anatomical structure to be segmented. Highly
// homogeneous regions may only require a couple of iterations. Regions
// with ramp effects, like MRI images with inhomogeneous fields, may
// require more iterations. In practice, it seems to be more important to
// carefully select the multiplier factor than the number of iterations.
// However, keep in mind that there is no guarantee that this
// algorithm will converge on a stable region. It is possible that by
// letting the algorithm run for more iterations the region will end up
// engulfing the entire image.
//
// \index{itk::ConfidenceConnectedImageFilter!SetNumberOfIterations()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
confidenceConnected->SetNumberOfIterations(5);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The output of this filter is a binary image with zero-value pixels
// everywhere except on the extracted region. The intensity value to be
// set inside the region is selected with the method
// \code{SetReplaceValue()}.
//
// \index{itk::ConfidenceConnectedImageFilter!SetReplaceValue()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
confidenceConnected->SetReplaceValue(255);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The initialization of the algorithm requires the user to provide a seed
// point. It is convenient to select this point to be placed in a
// \emph{typical} region of the anatomical structure to be segmented. A
// small neighborhood around the seed point will be used to compute the
// initial mean and standard deviation for the inclusion criterion. The
// seed is passed in the form of an \doxygen{Index} to the \code{SetSeed()}
// method.
//
// \index{itk::ConfidenceConnectedImageFilter!SetSeed()}
// \index{itk::ConfidenceConnectedImageFilter!SetInitialNeighborhoodRadius()}
//
// Software Guide : EndLatex
index[0] = std::stoi(argv[3]);
index[1] = std::stoi(argv[4]);
// Software Guide : BeginCodeSnippet
confidenceConnected->SetSeed(index);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The size of the initial neighborhood around the seed is defined with the
// method \code{SetInitialNeighborhoodRadius()}. The neighborhood will be
// defined as an $N$-dimensional rectangular region with $2r+1$ pixels on
// the side, where $r$ is the value passed as initial neighborhood radius.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
confidenceConnected->SetInitialNeighborhoodRadius(2);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The invocation of the \code{Update()} method on the writer triggers the
// execution of the pipeline. It is recommended to place update calls in a
// \code{try/catch} block in case errors occur and exceptions are thrown.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
try
{
writer->Update();
}
catch (const itk::ExceptionObject & excep)
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
// Software Guide : EndCodeSnippet
// clang-format off
// Software Guide : BeginLatex
//
// Let's now run this example using as input the image
// \code{BrainProtonDensitySlice.png} provided in the directory
// \code{Examples/Data}. We can easily segment the major anatomical
// structures by providing seeds in the appropriate locations. For example
//
// \begin{center}
// \begin{tabular}{|l|c|c|}
// \hline
// Structure & Seed Index & Output Image \\ \hline
// White matter & $(60,116)$ & Second from left in Figure \ref{fig:ConfidenceConnectedOutput} \\ \hline
// Ventricle & $(81,112)$ & Third from left in Figure \ref{fig:ConfidenceConnectedOutput} \\ \hline
// Gray matter & $(107,69)$ & Fourth from left in Figure \ref{fig:ConfidenceConnectedOutput} \\ \hline
// \end{tabular}
// \end{center}
//
// \begin{figure} \center
// \includegraphics[width=0.24\textwidth]{BrainProtonDensitySlice}
// \includegraphics[width=0.24\textwidth]{ConfidenceConnectedOutput1}
// \includegraphics[width=0.24\textwidth]{ConfidenceConnectedOutput2}
// \includegraphics[width=0.24\textwidth]{ConfidenceConnectedOutput3}
// \itkcaption[ConfidenceConnected segmentation results]{Segmentation results
// for the ConfidenceConnected filter for various seed points.}
// \label{fig:ConfidenceConnectedOutput}
// \end{figure}
//
// Note that the gray matter is not being completely segmented. This
// illustrates the vulnerability of the region growing methods when the
// anatomical structures to be segmented do not have a homogeneous
// statistical distribution over the image space. You may want to
// experiment with different numbers of iterations to verify how the
// accepted region will extend.
//
// Software Guide : EndLatex
// clang-format on
return EXIT_SUCCESS;
}
itk::CurvatureFlowImageFilter
Denoise an image using curvature driven flow.
Definition: itkCurvatureFlowImageFilter.h:95
itk::CastImageFilter
Casts input pixels to output pixel type.
Definition: itkCastImageFilter.h:104
itkImageFileReader.h
itkCastImageFilter.h
itk::ImageFileReader
Data source that reads image data from a single file.
Definition: itkImageFileReader.h:75
itk::GTest::TypedefsAndConstructors::Dimension2::IndexType
ImageBaseType::IndexType IndexType
Definition: itkGTestTypedefsAndConstructors.h:50
itk::ImageFileWriter
Writes image data to a single file.
Definition: itkImageFileWriter.h:87
itk::ConfidenceConnectedImageFilter
Segment pixels with similar statistics using connectivity.
Definition: itkConfidenceConnectedImageFilter.h:63
itkConfidenceConnectedImageFilter.h
itkCurvatureFlowImageFilter.h
itkImageFileWriter.h
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:86
itk::GTest::TypedefsAndConstructors::Dimension2::Dimension
constexpr unsigned int Dimension
Definition: itkGTestTypedefsAndConstructors.h:44