/*=========================================================================
 *
 *  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.
 *
 *=========================================================================*/

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImageSeriesReader.h"
#include "itkImageSeriesWriter.h"
#include "itkNumericSeriesFileNames.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkTestingMacros.h"
#include "itkGDCMImageIO.h"

int
itkGDCMImageReadSeriesWriteTest(int argc, char * argv[])
{
  if (argc < 4)
  {
    std::cerr << "Usage: " << itkNameOfTestExecutableMacro(argv);
    std::cerr << " InputImage OutputDicomDirectory SingleOutputImage" << std::endl;
    return EXIT_FAILURE;
  }
  const char * inputImage = argv[1];
  const char * outputDirectory = argv[2];
  const char * singleOutputImage = argv[3];

  using PixelType = short;
  constexpr unsigned int Dimension = 3;

  using ImageType = itk::Image<PixelType, Dimension>;
  using ReaderType = itk::ImageFileReader<ImageType>;

  auto reader = ReaderType::New();

  reader->SetFileName(inputImage);

  ITK_TRY_EXPECT_NO_EXCEPTION(reader->Update());

  using ImageIOType = itk::GDCMImageIO;
  using NamesGeneratorType = itk::NumericSeriesFileNames;

  auto gdcmIO = ImageIOType::New();

  itksys::SystemTools::MakeDirectory(outputDirectory);

  using OutputPixelType = short;
  constexpr unsigned int OutputDimension = 2;

  using Image2DType = itk::Image<OutputPixelType, OutputDimension>;
  using SeriesWriterType = itk::ImageSeriesWriter<ImageType, Image2DType>;

  auto namesGenerator = NamesGeneratorType::New();

  itk::MetaDataDictionary & dict = gdcmIO->GetMetaDataDictionary();
  std::string               tagkey, value;
  tagkey = "0008|0060"; // Modality
  value = "MR";
  itk::EncapsulateMetaData<std::string>(dict, tagkey, value);
  tagkey = "0008|0008"; // Image Type
  value = "DERIVED\\SECONDARY";
  itk::EncapsulateMetaData<std::string>(dict, tagkey, value);
  tagkey = "0008|0064"; // Conversion Type
  value = "DV";
  itk::EncapsulateMetaData<std::string>(dict, tagkey, value);


  auto seriesWriter = SeriesWriterType::New();
  seriesWriter->SetInput(reader->GetOutput());
  seriesWriter->SetImageIO(gdcmIO);
  ITK_TEST_SET_GET_VALUE(gdcmIO, seriesWriter->GetImageIO());

  ImageType::RegionType region = reader->GetOutput()->GetLargestPossibleRegion();
  ImageType::IndexType  start = region.GetIndex();
  ImageType::SizeType   size = region.GetSize();


  std::string format = outputDirectory;
  format += "/image%03d.dcm";

  namesGenerator->SetSeriesFormat(format.c_str());
  namesGenerator->SetStartIndex(start[2]);
  namesGenerator->SetEndIndex(start[2] + size[2] - 1);
  namesGenerator->SetIncrementIndex(1);

  seriesWriter->SetFileNames(namesGenerator->GetFileNames());

  ITK_TRY_EXPECT_NO_EXCEPTION(seriesWriter->Update());


  // Now read back in and write out as 3D image for comparison with the input.
  using SeriesReaderType = itk::ImageSeriesReader<ImageType>;
  auto seriesReader = SeriesReaderType::New();
  seriesReader->SetFileNames(namesGenerator->GetFileNames());

  using SingleWriterType = itk::ImageFileWriter<ImageType>;
  auto singleWriter = SingleWriterType::New();
  singleWriter->SetInput(seriesReader->GetOutput());
  singleWriter->SetFileName(singleOutputImage);

  ITK_TRY_EXPECT_NO_EXCEPTION(singleWriter->Update());

  return EXIT_SUCCESS;
}