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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
//
//  This example illustrates how to read a single DICOM slice and write it
//  back as another DICOM slice. In the process an intensity rescaling is also
//  applied.
//
//  In order to read and write the slice we use the \doxygen{GDCMImageIO}
//  class which encapsulates a connection to the underlying GDCM library. In
//  this way we gain access from ITK to the DICOM functionalities offered by
//  GDCM. The GDCMImageIO object is connected as the ImageIO object to be used
//  by the \doxygen{ImageFileWriter}.
//
//  We should first include the following header files.
//
//  Software Guide : EndLatex

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

#include <list>
#include <fstream>

int
main(int argc, char * argv[])
{

  // Verify the number of parameters in the command line
  if (argc < 5)
  {
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0] << " DicomImage OutputDicomImage ";
    std::cerr << " OutputImage RescaleDicomImage\n";
    return EXIT_FAILURE;
  }

  // Software Guide : BeginLatex
  //
  // Then we declare the pixel type and image dimension, and use them for
  // instantiating the image type to be read.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using InputPixelType = signed short;
  constexpr unsigned int InputDimension = 2;

  using InputImageType = itk::Image<InputPixelType, InputDimension>;
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // With the image type we can instantiate the type of the reader, create
  // one, and set the filename of the image to be read.
  //
  // Software Guide : EndLatex

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

  ReaderType::Pointer reader = ReaderType::New();
  reader->SetFileName(argv[1]);
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // GDCMImageIO is an ImageIO class for reading and writing DICOM v3 and
  // ACR/NEMA images. The GDCMImageIO object is constructed here and connected
  // to the ImageFileReader.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using ImageIOType = itk::GDCMImageIO;

  ImageIOType::Pointer gdcmImageIO = ImageIOType::New();

  reader->SetImageIO(gdcmImageIO);
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // At this point we can trigger the reading process by invoking the
  // \code{Update()} method.  Since this reading process may eventually throw
  // an exception, we place the invocation inside a \code{try/catch} block.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  try
  {
    reader->Update();
  }
  catch (const itk::ExceptionObject & e)
  {
    std::cerr << "exception in file reader " << std::endl;
    std::cerr << e << std::endl;
    return EXIT_FAILURE;
  }
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // We now have the image in memory and can get access to it using the
  // \code{GetOutput()} method of the reader. In the remainder of this current
  // example, we focus on showing how to save this image again in DICOM
  // format in a new file.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginLatex
  //
  // First, we must instantiate an ImageFileWriter type. Then, we construct
  // one, set the filename to be used for writing, and connect the input image
  // to be written. Since in this example we write the image in different
  // ways, and in each case use a different writer, we enumerated the variable
  // names of the writer objects as well as their types.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using Writer1Type = itk::ImageFileWriter<InputImageType>;

  Writer1Type::Pointer writer1 = Writer1Type::New();

  writer1->SetFileName(argv[2]);
  writer1->SetInput(reader->GetOutput());
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  We need to explicitly set the proper image IO (GDCMImageIO) to the
  //  writer filter since the input DICOM dictionary is being passed along the
  //  writing process. The dictionary contains all necessary information that
  //  a valid DICOM file should contain, like Patient Name, Patient ID,
  //  Institution Name, etc.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  writer1->SetImageIO(gdcmImageIO);
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // The writing process is triggered by invoking the \code{Update()} method.
  // Since this execution may result in exceptions being thrown we place the
  // \code{Update()} call inside a \code{try/catch} block.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  try
  {
    writer1->Update();
  }
  catch (const itk::ExceptionObject & e)
  {
    std::cerr << "exception in file writer " << std::endl;
    std::cerr << e << std::endl;
    return EXIT_FAILURE;
  }
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  //  We will now rescale the image using the RescaleIntensityImageFilter. For
  //  this purpose we use a better suited pixel type: \code{unsigned char}
  //  instead of \code{signed short}.  The minimum and maximum values of the
  //  output image are explicitly defined in the rescaling filter.
  //
  // Software Guide : EndLatex

  //  Software Guide : BeginCodeSnippet
  using WritePixelType = unsigned char;

  using WriteImageType = itk::Image<WritePixelType, 2>;

  using RescaleFilterType =
    itk::RescaleIntensityImageFilter<InputImageType, WriteImageType>;

  RescaleFilterType::Pointer rescaler = RescaleFilterType::New();

  rescaler->SetOutputMinimum(0);
  rescaler->SetOutputMaximum(255);
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // We create a second writer object that will save the rescaled image into a
  // new file, which is not in DICOM format. This is done only for the sake of
  // verifying the image against the one that will be saved in DICOM format
  // later in this example.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using Writer2Type = itk::ImageFileWriter<WriteImageType>;

  Writer2Type::Pointer writer2 = Writer2Type::New();

  writer2->SetFileName(argv[3]);

  rescaler->SetInput(reader->GetOutput());
  writer2->SetInput(rescaler->GetOutput());
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // The writer can be executed by invoking the \code{Update()} method from
  // inside a \code{try/catch} block.
  //
  // Software Guide : EndLatex


  try
  {
    writer2->Update();
  }
  catch (const itk::ExceptionObject & e)
  {
    std::cerr << "exception in file writer " << std::endl;
    std::cerr << e << std::endl;
    return EXIT_FAILURE;
  }

  // Software Guide : BeginLatex
  //
  // We proceed now to save the same rescaled image into a file in DICOM
  // format. For this purpose we just need to set up a
  // \doxygen{ImageFileWriter} and pass to it the rescaled image as input.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using Writer3Type = itk::ImageFileWriter<WriteImageType>;

  Writer3Type::Pointer writer3 = Writer3Type::New();

  writer3->SetFileName(argv[4]);
  writer3->SetInput(rescaler->GetOutput());
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  // We now need to explicitly set the proper image IO (GDCMImageIO), but also
  // we must tell the ImageFileWriter to not use the MetaDataDictionary from
  // the input but from the GDCMImageIO since this is the one that contains
  // the DICOM specific information
  //
  // The GDCMImageIO object will automatically detect the pixel type, in this
  // case \code{unsigned char} and it will update the DICOM header information
  // accordingly.
  // \index{itk::ImageFileWriter!UseInputMetaDataDictionaryOff()}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  writer3->UseInputMetaDataDictionaryOff();
  writer3->SetImageIO(gdcmImageIO);
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Finally we trigger the execution of the DICOM writer by invoking the
  // Update() method from inside a try/catch block.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  try
  {
    writer3->Update();
  }
  catch (const itk::ExceptionObject & e)
  {
    std::cerr << "Exception in file writer " << std::endl;
    std::cerr << e << std::endl;
    return EXIT_FAILURE;
  }
  // Software Guide : EndCodeSnippet

  return EXIT_SUCCESS;
}