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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: {BinaryThresholdImageFilterOutput.png}
// ARGUMENTS:    150 180 0 255
// Software Guide : EndCommandLineArgs

// Software Guide : BeginLatex
//
//  \begin{figure}[h]
//    \centering
//    \includegraphics[width=7cm]{BinaryThresholdTransferFunction}
//    \caption[BinaryThresholdImageFilter transfer function]
//            {Transfer function of the BinaryThresholdImageFilter.
//            \label{fig:BinaryThresholdTransferFunction}}
//  \end{figure}
//
// This example illustrates the use of the binary threshold image filter.
// This filter is used to transform an image into a binary image by changing
// the pixel values according to the rule illustrated in
// Figure~\ref{fig:BinaryThresholdTransferFunction}. The user defines two
// thresholds---Upper and Lower---and two intensity values---Inside and
// Outside. For each pixel in the input image, the value of the pixel is
// compared with the lower and upper thresholds. If the pixel value is inside
// the range defined by $[\text{Lower},\text{Upper}]$ the output pixel is
// assigned the InsideValue. Otherwise the output pixels are assigned to the
// OutsideValue. Thresholding is commonly applied as the last operation of a
// segmentation pipeline.
//
// \index{itk::Binary\-Threshold\-Image\-Filter!Instantiation}
// \index{itk::Binary\-Threshold\-Image\-Filter!Header}
//
// The first step required to use the \doxygen{BinaryThresholdImageFilter} is
// to include its header file.
//
// Software Guide : EndLatex

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

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

int
main(int argc, char * argv[])
{
  if (argc < 7)
  {
    std::cerr << "Usage: " << argv[0];
    std::cerr << " inputImageFile outputImageFile ";
    std::cerr << " lowerThreshold upperThreshold ";
    std::cerr << " outsideValue insideValue   " << std::endl;
    return EXIT_FAILURE;
  }

  //  Software Guide : BeginLatex
  //
  //  The next step is to decide which pixel types to use for the input and
  //  output images.
  //
  //  Software Guide : EndLatex

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


  //  Software Guide : BeginLatex
  //
  //  The input and output image types are now defined using their respective
  //  pixel types and dimensions.
  //
  //  Software Guide : EndLatex

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


  //  Software Guide : BeginLatex
  //
  //  The filter type can be instantiated using the input and output image
  //  types defined above.
  //
  //  Software Guide : EndLatex

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


  //  Software Guide : BeginLatex
  //
  //  An \doxygen{ImageFileReader} class is also instantiated in order to read
  //  image data from a file. (See Section \ref{sec:IO} on page
  //  \pageref{sec:IO} for more information about reading
  //  and writing data.)
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using ReaderType = itk::ImageFileReader<InputImageType>;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  // An \doxygen{ImageFileWriter} is instantiated in order to write the output
  // image to a file.
  //
  //  Software Guide : EndLatex


  // Software Guide : BeginCodeSnippet
  using WriterType = itk::ImageFileWriter<OutputImageType>;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Both the filter and the reader are created by invoking their
  //  \code{New()} methods and assigning the result to
  //  \doxygen{SmartPointer}s.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  auto reader = ReaderType::New();
  auto filter = FilterType::New();
  // Software Guide : EndCodeSnippet

  auto writer = WriterType::New();
  writer->SetInput(filter->GetOutput());
  reader->SetFileName(argv[1]);


  //  Software Guide : BeginLatex
  //
  //  The image obtained with the reader is passed as input to the
  //  BinaryThresholdImageFilter.
  //
  //  \index{itk::Binary\-Threshold\-Image\-Filter!SetInput()}
  //  \index{itk::FileImageReader!GetOutput()}
  //
  //  Software Guide : EndLatex

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


  //  Software Guide : BeginLatex
  //
  //  The method \code{SetOutsideValue()} defines the intensity value to be
  //  assigned to those pixels whose intensities are outside the range defined
  //  by the lower and upper thresholds. The method \code{SetInsideValue()}
  //  defines the intensity value to be assigned to pixels with intensities
  //  falling inside the threshold range.
  //
  //  \index{itk::Binary\-Threshold\-Image\-Filter!SetOutsideValue()}
  //  \index{itk::Binary\-Threshold\-Image\-Filter!SetInsideValue()}
  //  \index{SetOutsideValue()!itk::Binary\-Threshold\-Image\-Filter}
  //  \index{SetInsideValue()!itk::Binary\-Threshold\-Image\-Filter}
  //
  //  Software Guide : EndLatex

  const OutputPixelType outsideValue = std::stoi(argv[5]);
  const OutputPixelType insideValue = std::stoi(argv[6]);

  // Software Guide : BeginCodeSnippet
  filter->SetOutsideValue(outsideValue);
  filter->SetInsideValue(insideValue);
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  The methods \code{SetLowerThreshold()} and \code{SetUpperThreshold()}
  //  define the range of the input image intensities that will be transformed
  //  into the \code{InsideValue}. Note that the lower and upper thresholds
  //  are values of the type of the input image pixels, while the inside and
  //  outside values are of the type of the output image pixels.
  //
  //  Software Guide : EndLatex

  const InputPixelType lowerThreshold = std::stoi(argv[3]);
  const InputPixelType upperThreshold = std::stoi(argv[4]);

  // Software Guide : BeginCodeSnippet
  filter->SetLowerThreshold(lowerThreshold);
  filter->SetUpperThreshold(upperThreshold);
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  The execution of the filter is triggered by invoking the \code{Update()}
  //  method.   If the filter's output has been passed as input to subsequent
  //  filters, the \code{Update()} call on any downstream filters in the
  //  pipeline will indirectly trigger the update of this filter.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  filter->Update();
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  // \begin{figure}
  // \center
  // \includegraphics[width=0.44\textwidth]{BrainProtonDensitySlice}
  // \includegraphics[width=0.44\textwidth]{BinaryThresholdImageFilterOutput}
  // \itkcaption[BinaryThresholdImageFilter output]{Effect of the
  // BinaryThresholdImageFilter on a slice from a MRI proton density image  of
  // the brain.} \label{fig:BinaryThresholdImageFilterInputOutput}
  // \end{figure}
  //
  //  Figure \ref{fig:BinaryThresholdImageFilterInputOutput} illustrates the
  //  effect of this filter on a MRI proton density image of the brain. This
  //  figure shows the limitations of the filter for performing segmentation
  //  by itself. These limitations are particularly noticeable in noisy images
  //  and in images lacking spatial uniformity as is the case with MRI due to
  //  field bias.
  //
  //  \relatedClasses
  //  \begin{itemize}
  //  \item \doxygen{ThresholdImageFilter}
  //  \end{itemize}
  //
  //  Software Guide : EndLatex

  writer->SetFileName(argv[2]);
  writer->Update();

  return EXIT_SUCCESS;
}
