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 *
 *  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
 *
 *         https://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}
//    OUTPUTS: {MedianImageFilterOutput.png}
//  Software Guide : EndCommandLineArgs

//  Software Guide : BeginLatex
//
//  The \doxygen{MedianImageFilter} is commonly used as a robust approach for
//  noise reduction. This filter is particularly efficient against
//  \emph{salt-and-pepper} noise. In other words, it is robust to the presence
//  of gray-level outliers. MedianImageFilter computes the value of each
//  output pixel as the statistical median of the neighborhood of values
//  around the corresponding input pixel. The following figure illustrates the
//  local effect of this filter in a $2D$ case. The statistical median of the
//  neighborhood on the left is passed as the output value associated with the
//  pixel at the center of the neighborhood.
//
//
//  \begin{center}
//  \begin{picture}(200,46)
//  \put(   5.0,  0.0 ){\framebox(30.0,15.0){25}}
//  \put(  35.0,  0.0 ){\framebox(30.0,15.0){30}}
//  \put(  65.0,  0.0 ){\framebox(30.0,15.0){32}}
//  \put(   5.0, 15.0 ){\framebox(30.0,15.0){27}}
//  \put(  35.0, 15.0 ){\framebox(30.0,15.0){25}}
//  \put(  65.0, 15.0 ){\framebox(30.0,15.0){29}}
//  \put(   5.0, 30.0 ){\framebox(30.0,15.0){28}}
//  \put(  35.0, 30.0 ){\framebox(30.0,15.0){26}}
//  \put(  65.0, 30.0 ){\framebox(30.0,15.0){50}}
//  \put( 100.0, 22.0 ){\vector(1,0){20.0}}
//  \put( 125.0, 15.0 ){\framebox(30.0,15.0){28}}
//  \end{picture}
//  \end{center}
//
//
//  This filter will work on images of any dimension thanks to the internal
//  use of \doxygen{NeighborhoodIterator} and
//  \doxygen{NeighborhoodOperator}. The size of the neighborhood over which
//  the median is computed can be set by the user.
//
//  \index{itk::MedianImageFilter}
//
//  Software Guide : EndLatex


#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"


//  Software Guide : BeginLatex
//
//  The header file corresponding to this filter should be included first.
//
//  \index{itk::MedianImageFilter!header}
//
//  Software Guide : EndLatex


// Software Guide : BeginCodeSnippet
#include "itkMedianImageFilter.h"
// Software Guide : EndCodeSnippet


int
main(int argc, char * argv[])
{
  if (argc < 3)
  {
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0] << "  inputImageFile   outputImageFile" << std::endl;
    return EXIT_FAILURE;
  }


  //  Software Guide : BeginLatex
  //
  //  Then the pixel and image types of the input and output must be defined.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using InputPixelType = unsigned char;
  using OutputPixelType = unsigned char;

  using InputImageType = itk::Image<InputPixelType, 2>;
  using OutputImageType = itk::Image<OutputPixelType, 2>;
  // Software Guide : EndCodeSnippet


  using ReaderType = itk::ImageFileReader<InputImageType>;
  using WriterType = itk::ImageFileWriter<OutputImageType>;

  auto reader = ReaderType::New();
  auto 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::MedianImageFilter!instantiation}
  //  \index{itk::MedianImageFilter!New()}
  //  \index{itk::MedianImageFilter!Pointer}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using FilterType = itk::MedianImageFilter<InputImageType, OutputImageType>;

  auto 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::MedianImageFilter!Radius}
  //  \index{itk::MedianImageFilter!Neighborhood}
  //
  //  Software Guide : EndLatex


  // Software Guide : BeginCodeSnippet
  InputImageType::SizeType indexRadius;

  indexRadius[0] = 1; // radius along x
  indexRadius[1] = 1; // radius along y

  filter->SetRadius(indexRadius);
  // 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::MedianImageFilter!SetInput()}
  //  \index{itk::MedianImageFilter!GetOutput()}
  //
  //  Software Guide : EndLatex


  // Software Guide : BeginCodeSnippet
  filter->SetInput(reader->GetOutput());
  writer->SetInput(filter->GetOutput());
  writer->Update();
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  // \begin{figure}
  // \center
  // \includegraphics[width=0.44\textwidth]{BrainProtonDensitySlice}
  // \includegraphics[width=0.44\textwidth]{MedianImageFilterOutput}
  // \itkcaption[Effect of the Median filter.]{Effect of the MedianImageFilter
  // on a slice from a MRI proton density brain image.}
  // \label{fig:MedianImageFilterOutput}
  // \end{figure}
  //
  //  Figure \ref{fig:MedianImageFilterOutput} illustrates the effect of the
  //  MedianImageFilter filter on a slice of MRI brain image using a
  //  neighborhood radius of
  //  \(1,1\), which corresponds to a $ 3 \times 3 $ classical neighborhood.
  //  The filtered image demonstrates the moderate tendency of the median
  //  filter to preserve edges.
  //
  //  Software Guide : EndLatex


  return EXIT_SUCCESS;
}
