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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
 *
 *         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,
 *  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 : BeginLatex
//
//  The classes responsible for reading and writing images are located at the
//  beginning and end of the data processing pipeline. These classes are
//  known as data sources (readers) and data sinks (writers).
//  Generally speaking they are referred to as filters, although readers have
//  no pipeline input and writers have no pipeline output.
//
//  The reading of images is managed by the class \doxygen{ImageFileReader}
//  while writing is performed by the class \doxygen{ImageFileWriter}. These
//  two classes are independent of any particular file format. The actual low
//  level task of reading and writing specific file formats is done behind
//  the scenes by a family of classes of type \doxygen{ImageIO}.
//
//  The first step for performing reading and writing is to include the
//  following headers.
//
//  \index{itk::ImageFileReader|textbf}
//  \index{itk::ImageFileReader!header}
//
//  \index{itk::ImageFileWriter|textbf}
//  \index{itk::ImageFileWriter!header}
//
//  Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
// Software Guide : EndCodeSnippet


#include "itkImage.h"


int
main(int argc, char ** argv)
{
  // Verify the number of parameters in the command line
  if (argc < 3)
  {
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0] << " inputImageFile  outputImageFile " << std::endl;
    return EXIT_FAILURE;
  }


  //  Software Guide : BeginLatex
  //
  //  Then, as usual, a decision must be made about the type of pixel used to
  //  represent the image processed by the pipeline. Note that when reading
  //  and writing images, the pixel type of the image \textbf{is not
  //  necessarily} the same as the pixel type stored in the file.  Your
  //  choice of the pixel type (and hence template parameter) should be
  //  driven mainly by two considerations:
  //
  //  \begin{itemize}
  //  \item It should be possible to cast the pixel type in the file to
  //  the pixel type you select. This casting will be performed using the
  //  standard C-language rules, so you will have to make sure that the
  //  conversion does not result in information being lost.
  //  \item The pixel type in memory should be appropriate to the type of
  //  processing you intend to apply on the images.
  //  \end{itemize}
  //
  //  A typical selection for medical images is illustrated in
  //  the following lines.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using PixelType = short;
  constexpr unsigned int Dimension = 2;
  using ImageType = itk::Image<PixelType, Dimension>;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Note that the dimension of the image in memory should match that of
  //  the image in the file. There are a couple of special cases in which this
  //  condition may be relaxed, but in general it is better to ensure that
  //  both dimensions match.
  //
  //  We can now instantiate the types of the reader and writer. These two
  //  classes are parameterized over the image type.
  //
  //  \index{itk::ImageFileReader!Instantiation}
  //  \index{itk::ImageFileWriter!Instantiation}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using ReaderType = itk::ImageFileReader<ImageType>;
  using WriterType = itk::ImageFileWriter<ImageType>;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Then, we create one object of each type using the New() method and
  //  assign the result to a \doxygen{SmartPointer}.
  //
  //  \index{itk::ImageFileReader!New()}
  //  \index{itk::ImageFileWriter!New()}
  //  \index{itk::ImageFileReader!SmartPointer}
  //  \index{itk::ImageFileWriter!SmartPointer}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  ReaderType::Pointer reader = ReaderType::New();
  WriterType::Pointer writer = WriterType::New();
  // Software Guide : EndCodeSnippet


  // Here we recover the file names from the command line arguments
  //
  const char * inputFilename = argv[1];
  const char * outputFilename = argv[2];


  //  Software Guide : BeginLatex
  //
  //  The name of the file to be read or written is passed to the
  //  SetFileName() method.
  //
  //  \index{itk::ImageFileReader!SetFileName()}
  //  \index{itk::ImageFileWriter!SetFileName()}
  //  \index{SetFileName()!itk::ImageFileReader}
  //  \index{SetFileName()!itk::ImageFileWriter}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  reader->SetFileName(inputFilename);
  writer->SetFileName(outputFilename);
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  We can now connect these readers and writers to filters to create a
  //  pipeline. For example, we can create a short pipeline by passing
  //  the output of the reader directly to the input of the writer.
  //
  //  Software Guide : EndLatex

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


  //  Software Guide : BeginLatex
  //
  //  At first glance this may look like a quite useless program, but it is
  //  actually implementing a powerful file format conversion tool! The
  //  execution of the pipeline is triggered by the invocation of the
  //  \code{Update()} methods in one of the final objects. In this case, the
  //  final data pipeline object is the writer. It is a wise practice of
  //  defensive programming to insert any \code{Update()} call inside a
  //  \code{try/catch} block in case exceptions are thrown during the
  //  execution of the pipeline.
  //
  //  Software Guide : EndLatex


  // Software Guide : BeginCodeSnippet
  try
  {
    writer->Update();
  }
  catch (const itk::ExceptionObject & err)
  {
    std::cerr << "ExceptionObject caught !" << std::endl;
    std::cerr << err << std::endl;
    return EXIT_FAILURE;
  }
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Note that exceptions should only be caught by pieces of code that know
  //  what to do with them. In a typical application this \code{catch} block
  //  should probably reside in the GUI code. The action on the \code{catch}
  //  block could inform the user about the failure of the IO operation.
  //
  //  The IO architecture of the toolkit makes it possible to avoid explicit
  //  specification of the file format used to read or write
  //  images.\footnote{In this example no file format is specified; this
  //  program can be used as a general file conversion utility.}  The object
  //  factory mechanism enables the ImageFileReader and ImageFileWriter to
  //  determine (at run-time) which file format it is working
  //  with. Typically, file formats are chosen based on the filename
  //  extension, but the architecture supports arbitrarily complex processes
  //  to determine whether a file can be read or written. Alternatively, the
  //  user can specify the data file format by explicit instantiation and
  //  assignment of the appropriate \doxygen{ImageIO} subclass.
  //
  //  For historical reasons and as a convenience to the user, the
  //  \doxygen{ImageFileWriter} also has a \code{Write()} method that is
  //  aliased to the \code{Update()} method. You can in principle use either
  //  of them but \code{Update()} is recommended since \code{Write()} may be
  //  deprecated in the future.
  //
  //  Software Guide : EndLatex

  return EXIT_SUCCESS;
}