/*=========================================================================
 *
 *  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 : BeginLatex
//
//  This example illustrates how to read a single DICOM slice and write it
//  back with some changed header information as another DICOM slice. Header
//  Key/Value pairs can be specified on the command line. The keys are defined
//  in the file
//
//  \code{Insight/Utilities/gdcm/Dicts/dicomV3.dic}.
//
//  Please note that modifying the content of a DICOM header is a very risky
//  operation. The header contains fundamental information about the patient
//  and therefore its consistency must be protected from any data corruption.
//  Before attempting to modify the DICOM headers of your files, you must make
//  sure that you have a very good reason for doing so, and that you can
//  ensure that this information change will not result in a lower quality of
//  health care being delivered to the patient.
//
//  \index{DICOM!Changing Headers}
//
//  Software Guide : EndLatex

// Software Guide : BeginLatex
//
// We must start by including the relevant header files. Here we include the
// image reader, image writer, the image, the metadata dictionary and its
// entries, the metadata objects and the GDCMImageIO. The metadata dictionary
// is the data container that stores all the entries from the DICOM header
// once the DICOM image file is read into an ITK image.
//
// Software Guide : EndLatex

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

#include <list>
#include <fstream>

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

  if (argc < 5)
  {
    std::cerr << "Usage: " << argv[0]
              << " DicomImage OutputDicomImage Entry Value\n";
    return EXIT_FAILURE;
  }

  // Software Guide : BeginLatex
  //
  // We declare the image type by selecting a particular pixel type and image
  // dimension.
  //
  // Software Guide : EndLatex

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

  // Software Guide : BeginLatex
  //
  // We instantiate the reader type by using the image type as template
  // parameter. An instance of the reader is created and the file name to be
  // read is taken from the command line arguments.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using ReaderType = itk::ImageFileReader<InputImageType>;
  auto reader = ReaderType::New();
  reader->SetFileName(argv[1]);
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // The GDCMImageIO object is created in order to provide the services for
  // reading and writing DICOM files. The newly created image IO class is
  // connected to the reader.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using ImageIOType = itk::GDCMImageIO;
  auto gdcmImageIO = ImageIOType::New();
  reader->SetImageIO(gdcmImageIO);
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // The reading of the image is triggered by invoking \code{Update()} in the
  // reader.
  //
  // Software Guide : EndLatex


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

  // Software Guide : BeginLatex
  //
  // We take the metadata dictionary from the image that the reader had loaded
  // in memory.
  //
  // Software Guide : EndLatex


  // Software Guide : BeginCodeSnippet
  InputImageType::Pointer inputImage = reader->GetOutput();
  using DictionaryType = itk::MetaDataDictionary;
  DictionaryType & dictionary = inputImage->GetMetaDataDictionary();
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Now we access the entries in the metadata dictionary, and for particular
  // key values we assign a new content to the entry. This is done here by
  // taking
  // \{key,value\} pairs from the command line arguments. The relevant method
  // is \code{EncapsulateMetaData} that takes the dictionary and for a given
  // key provided by \code{entryId}, replaces the current value with the
  // content of the \code{value} variable. This is repeated for every
  // potential pair present in the command line arguments.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  for (int i = 3; i < argc; i += 2)
  {
    std::string entryId(argv[i]);
    std::string value(argv[i + 1]);
    itk::EncapsulateMetaData<std::string>(dictionary, entryId, value);
  }
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Now that the dictionary has been updated, we proceed to save the image.
  // This output image will have the modified data associated with its DICOM
  // header.
  //
  // Using the image type, we instantiate a writer type and construct a
  // writer. A short pipeline between the reader and the writer is connected.
  // The filename to write is taken from the command line arguments. The image
  // IO object is connected to the writer.
  //
  // Software Guide : EndLatex

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

  auto writer1 = Writer1Type::New();

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


  // Software Guide : BeginLatex
  //
  // Execution of the writer is triggered by invoking the \code{Update()}
  // method.
  //
  // Software Guide : EndLatex

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

  // Software Guide : BeginLatex
  //
  // Remember again, that modifying the header entries of a DICOM file
  // involves very serious risks for patients and therefore must be done with
  // extreme caution.
  //
  // Software Guide : EndLatex


  return EXIT_SUCCESS;
}
