ITK  5.2.0
Insight Toolkit
Examples/Filtering/VotingBinaryIterativeHoleFillingImageFilter.cxx
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*
* Copyright NumFOCUS
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* 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
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* 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,
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* See the License for the specific language governing permissions and
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*=========================================================================*/
// Software Guide : BeginCommandLineArgs
// INPUTS: {BinaryThresholdImageFilterOutput.png}
// OUTPUTS: {VotingBinaryIterativeHoleFillingImageFilterOutput1.png}
// ARGUMENTS: 1 1 20
// Software Guide : EndCommandLineArgs
// Software Guide : BeginCommandLineArgs
// INPUTS: {BinaryThresholdImageFilterOutput.png}
// OUTPUTS: {VotingBinaryIterativeHoleFillingImageFilterOutput2.png}
// ARGUMENTS: 2 2 20
// Software Guide : EndCommandLineArgs
// Software Guide : BeginCommandLineArgs
// INPUTS: {BinaryThresholdImageFilterOutput.png}
// OUTPUTS: {VotingBinaryIterativeHoleFillingImageFilterOutput3.png}
// ARGUMENTS: 3 3 20
// Software Guide : EndCommandLineArgs
// Software Guide : BeginLatex
//
// The \doxygen{VotingBinaryIterativeHoleFillingImageFilter} applies a voting
// operation in order to fill in cavities. This can be used for smoothing
// contours and for filling holes in binary images. This filter runs
// a \doxygen{VotingBinaryHoleFillingImageFilter} internally until no
// pixels change or the maximum number of iterations has been reached.
//
// \index{itk::Voting\-Binary\-Iterative\-Hole\-Filling\-Image\-Filter}
//
// Software Guide : EndLatex
#include "itkImage.h"
// Software Guide : BeginLatex
//
// The header file corresponding to this filter should be included first.
//
// \index{itk::Voting\-Binary\-Iterative\-Hole\-Filling\-Image\-Filter!header}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
int
main(int argc, char * argv[])
{
if (argc < 5)
{
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0]
<< " inputImageFile outputImageFile radiusX radiusY iterations"
<< std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// Then the pixel and image types must be defined. Note that this filter
// requires the input and output images to be of the same type, therefore a
// single image type is required for the template instantiation.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using PixelType = unsigned char;
using ImageType = itk::Image<PixelType, 2>;
// Software Guide : EndCodeSnippet
using ReaderType = itk::ImageFileReader<ImageType>;
using WriterType = itk::ImageFileWriter<ImageType>;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
reader->SetFileName(argv[1]);
writer->SetFileName(argv[2]);
// Software Guide : BeginLatex
//
// Using the image types, it is now possible to define the filter type
// and create the filter object.
//
// \index{itk::Voting\-Binary\-Iterative\-Hole\-Filling\-Image\-Filter!instantiation}
// \index{itk::Voting\-Binary\-Iterative\-Hole\-Filling\-Image\-Filter!New()}
// \index{itk::Voting\-Binary\-Iterative\-Hole\-Filling\-Image\-Filter!Pointer}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
using FilterType =
FilterType::Pointer filter = FilterType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The size of the neighborhood is defined along every dimension by
// passing a \code{SizeType} object with the corresponding values. The
// value on each dimension is used as the semi-size of a rectangular
// box. For example, in $2D$ a size of \(1,2\) will result in a $3 \times
// 5$ neighborhood.
//
// \index{itk::Voting\-Binary\-Iterative\-Hole\-Filling\-Image\-Filter!Radius}
// \index{itk::Voting\-Binary\-Iterative\-Hole\-Filling\-Image\-Filter!Neighborhood}
//
// Software Guide : EndLatex
const unsigned int radiusX = std::stoi(argv[3]);
const unsigned int radiusY = std::stoi(argv[4]);
// Software Guide : BeginCodeSnippet
ImageType::SizeType indexRadius;
indexRadius[0] = radiusX; // radius along x
indexRadius[1] = radiusY; // radius along y
filter->SetRadius(indexRadius);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Since the filter is expecting a binary image as input, we must specify
// the levels that are going to be considered background and foreground.
// This is done with the \code{SetForegroundValue()} and
// \code{SetBackgroundValue()} methods.
//
// \index{itk::Voting\-Binary\-Iterative\-Hole\-Filling\-Image\-Filter!SetForegroundValue()}
// \index{itk::Voting\-Binary\-Iterative\-Hole\-Filling\-Image\-Filter!SetBackgroundValue()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
filter->SetBackgroundValue(0);
filter->SetForegroundValue(255);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We must also specify the majority threshold that is going to be used as
// the decision criterion for converting a background pixel into a
// foreground pixel. The rule of conversion is that a background pixel will
// be converted into a foreground pixel if the number of foreground
// neighbors surpass the number of background neighbors by the majority
// value. For example, in a 2D image, with neighborhood of radius 1, the
// neighborhood will have size $3 \times 3$. If we set the majority value
// to 2, then we are requiring that the number of foreground neighbors
// should be at least (3x3 -1 )/2 + majority. This is done with the
// \code{SetMajorityThreshold()} method.
//
// \index{itk::Voting\-Binary\-Iterative\-Hole\-Filling\-Image\-Filter!SetMajorityThreshold()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
filter->SetMajorityThreshold(2);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Finally we specify the maximum number of iterations for which this
// filter should run. The number of iterations will determine the maximum
// size of holes and cavities that this filter will be able to fill. The
// more iterations you run, the larger the cavities that will be filled in.
//
// \index{itk::Voting\-Binary\-Iterative\-Hole\-Filling\-Image\-Filter!SetMaximumNumberOfIterations()}
//
// Software Guide : EndLatex
const unsigned int numberOfIterations = std::stoi(argv[5]);
// Software Guide : BeginCodeSnippet
filter->SetMaximumNumberOfIterations(numberOfIterations);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The input to the filter can be taken from any other filter, for example
// a reader. The output can be passed down the pipeline to other filters,
// for example, a writer. An update call on any downstream filter will
// trigger the execution of the median filter.
//
// \index{itk::Voting\-Binary\-Iterative\-Hole\-Filling\-Image\-Filter!SetInput()}
// \index{itk::Voting\-Binary\-Iterative\-Hole\-Filling\-Image\-Filter!GetOutput()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
filter->SetInput(reader->GetOutput());
writer->SetInput(filter->GetOutput());
writer->Update();
// Software Guide : EndCodeSnippet
const unsigned int iterationsUsed = filter->GetCurrentNumberOfIterations();
std::cout << "The filter used " << iterationsUsed << " iterations "
<< std::endl;
const unsigned int numberOfPixelsChanged =
filter->GetNumberOfPixelsChanged();
std::cout << "and changed a total of " << numberOfPixelsChanged << " pixels"
<< std::endl;
// Software Guide : BeginLatex
//
// \begin{figure}
// \center
// \includegraphics[width=0.44\textwidth]{BinaryThresholdImageFilterOutput}
// \includegraphics[width=0.44\textwidth]{VotingBinaryIterativeHoleFillingImageFilterOutput1}
// \includegraphics[width=0.44\textwidth]{VotingBinaryIterativeHoleFillingImageFilterOutput2}
// \includegraphics[width=0.44\textwidth]{VotingBinaryIterativeHoleFillingImageFilterOutput3}
// \itkcaption[Effect of the VotingBinaryIterativeHoleFilling
// filter.]{Effect of the VotingBinaryIterativeHoleFillingImageFilter on a
// slice from a MRI proton density brain image that has been thresholded in
// order to produce a binary image. The output images have used radius 1,2
// and 3 respectively.}
// \label{fig:VotingBinaryIterativeHoleFillingImageFilterOutput}
// \end{figure}
//
// Figure \ref{fig:VotingBinaryIterativeHoleFillingImageFilterOutput}
// illustrates the effect of the
// VotingBinaryIterativeHoleFillingImageFilter filter on a thresholded
// slice of MRI brain image using neighborhood radii of \(1,1\), \(2,2\)
// and \(3,3\) that correspond respectively to neighborhoods of size $ 3
// \times 3 $, $ 5 \times 5 $, $ 7 \times 7 $. The filtered image
// demonstrates the capability of this filter for reducing noise both in
// the background and foreground of the image, as well as smoothing the
// contours of the regions.
//
// Software Guide : EndLatex
return EXIT_SUCCESS;
}
itkImageFileReader.h
itk::GTest::TypedefsAndConstructors::Dimension2::SizeType
ImageBaseType::SizeType SizeType
Definition: itkGTestTypedefsAndConstructors.h:49
itkImage.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
itkImageFileWriter.h
itk::Image
Templated n-dimensional image class.
Definition: itkImage.h:86
itkVotingBinaryIterativeHoleFillingImageFilter.h
itk::VotingBinaryIterativeHoleFillingImageFilter
Fills in holes and cavities by iteratively applying a voting operation.
Definition: itkVotingBinaryIterativeHoleFillingImageFilter.h:56