/*=========================================================================
 *
 *  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 <fstream>
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkTestingComparisonImageFilter.h"
#include "itkExtractImageFilter.h"
#include "itkTestingMacros.h"

using PixelType = unsigned char;
using ImageType = itk::Image<PixelType, 3>;
using ImagePointer = ImageType::Pointer;

namespace
{

bool
SameImage(ImagePointer testImage, ImagePointer baselineImage)
{
  PixelType     intensityTolerance = 0;
  int           radiusTolerance = 0;
  unsigned long numberOfPixelTolerance = 0;

  using DiffType = itk::Testing::ComparisonImageFilter<ImageType, ImageType>;
  auto diff = DiffType::New();
  diff->SetValidInput(baselineImage);
  diff->SetTestInput(testImage);
  diff->SetDifferenceThreshold(intensityTolerance);
  diff->SetToleranceRadius(radiusTolerance);
  diff->UpdateLargestPossibleRegion();

  unsigned long status = diff->GetNumberOfPixelsWithDifferences();

  if (status > numberOfPixelTolerance)
  {
    return false;
  }

  return true;
}
} // namespace

int
itkImageFileWriterPastingTest3(int argc, char * argv[])
{
  if (argc < 3)
  {
    std::cerr << "Missing parameters." << std::endl;
    std::cerr << "Usage: " << itkNameOfTestExecutableMacro(argv);
    std::cerr << " input output" << std::endl;
    return EXIT_FAILURE;
  }

  // We remove the output file
  if (argc == 3)
  {
    itksys::SystemTools::RemoveFile(argv[2]);
  }
  else
  {
    // copy this file to over write
    itksys::SystemTools::CopyAFile(argv[3], argv[2]);
  }


  using ReaderType = itk::ImageFileReader<ImageType>;
  using WriterType = itk::ImageFileWriter<ImageType>;


  ImageType::Pointer image;

  // update just a specific region
  // Then let the reader go out of scope to orphan the image to have
  // no source.
  {
    auto reader = ReaderType::New();
    reader->SetFileName(argv[1]);
    reader->SetUseStreaming(true);
    reader->UpdateOutputInformation();

    ImageType::RegionType largestRegion = reader->GetOutput()->GetLargestPossibleRegion();

    ImageType::RegionType ioRegion;
    ImageType::IndexType  ioIndex;
    ioIndex[0] = largestRegion.GetIndex()[0] + largestRegion.GetSize()[0] / 3;
    ioIndex[1] = largestRegion.GetIndex()[1] + largestRegion.GetSize()[1] / 3;
    ioIndex[2] = largestRegion.GetIndex()[2] + largestRegion.GetSize()[2] / 3;
    ImageType::SizeType ioSize;
    ioSize[0] = largestRegion.GetSize()[0] / 3;
    ioSize[1] = largestRegion.GetSize()[1] / 3;
    ioSize[2] = largestRegion.GetSize()[2] / 3;
    ioRegion = ImageType::RegionType(ioIndex, ioSize);

    image = reader->GetOutput();

    image->SetRequestedRegion(ioRegion);
    image->Update();
  }

  // Setup the writer with an image which doesn't have a source
  //
  // We expect that the writer should respect the LargestPossibleRegion
  auto writer = WriterType::New();
  writer->SetFileName(argv[2]);
  writer->SetInput(image);

  // convert the buffered region of the image into an io region
  itk::ImageIORegion ioRegion(3);
  itk::ImageIORegionAdaptor<ImageType::ImageDimension>::Convert(
    image->GetBufferedRegion(), ioRegion, image->GetLargestPossibleRegion().GetIndex());
  writer->SetIORegion(ioRegion);

  ITK_TRY_EXPECT_NO_EXCEPTION(writer->Update());


  auto reader = ReaderType::New();
  reader->SetFileName(argv[1]);
  reader->UpdateOutputInformation();

  auto readerTestImage = ReaderType::New();
  readerTestImage->SetFileName(argv[2]);
  readerTestImage->UpdateOutputInformation();

  // Test that the size of the two images are the same
  if (reader->GetOutput()->GetLargestPossibleRegion() != readerTestImage->GetOutput()->GetLargestPossibleRegion())
  {
    std::cerr << "Image size don't match!" << std::endl;
    std::cerr << "Input size: " << reader->GetOutput()->GetLargestPossibleRegion()
              << "Output size: " << readerTestImage->GetOutput()->GetLargestPossibleRegion() << std::endl;
    return EXIT_FAILURE;
  }

  // compare the two subregions
  using ExtractImageFilterType = itk::ExtractImageFilter<ImageType, ImageType>;
  auto extractTestImage = ExtractImageFilterType::New();
  extractTestImage->SetInput(readerTestImage->GetOutput());
  extractTestImage->SetDirectionCollapseToSubmatrix();
  extractTestImage->SetExtractionRegion(image->GetBufferedRegion());
  extractTestImage->InPlaceOn();

  using ExtractImageFilterType = itk::ExtractImageFilter<ImageType, ImageType>;
  auto extractBaselineImage = ExtractImageFilterType::New();
  extractBaselineImage->SetInput(reader->GetOutput());
  extractBaselineImage->SetDirectionCollapseToSubmatrix();
  extractBaselineImage->SetExtractionRegion(image->GetBufferedRegion());
  extractBaselineImage->InPlaceOn();


  if (!SameImage(extractTestImage->GetOutput(), extractBaselineImage->GetOutput()))
  {
    std::cerr << "input paste and output paste regions don't match!\n";
    return EXIT_FAILURE;
  }

  return EXIT_SUCCESS;
}