/*=========================================================================
 *
 *  Copyright UMC Utrecht and contributors
 *
 *  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.
 *
 *=========================================================================*/
/** \file
 \brief Compare two images.

 \verbinclude imagecompare.help
 */
#include "itkCommandLineArgumentParser.h"

#include "itkNumericTraits.h"
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkExtractImageFilter.h"
#include "itksys/SystemTools.hxx"

#include "itkImageSource.h" // This should not be necessary after ITK patch is merged
#include "itkTestingComparisonImageFilter.h"

/**
 * ******************* GetHelpString *******************
 */

std::string
GetHelpString()
{
  return "Usage:\n"
         "elxImageCompare\n"
         "  -test      image filename to test against baseline\n"
         "  -base      baseline image filename\n"
         "  [-t]       intensity difference threshold, default 0\n"
         "  [-a]       allowable tolerance (# voxels different), default 0";

} // end GetHelpString()


// This comparison works on all image types by reading images in a 6D double images. If images > 6 dimensions
// must be compared, change this variable.
static const unsigned int ITK_TEST_DIMENSION_MAX = 4;

int
main(int argc, char ** argv)
{
  auto parser = itk::CommandLineArgumentParser::New();
  parser->SetCommandLineArguments(argc, argv);
  parser->SetProgramHelpText(GetHelpString());

  parser->MarkArgumentAsRequired("-test", "The input filename.");
  parser->MarkArgumentAsRequired("-base", "The baseline image filename.");

  itk::CommandLineArgumentParser::ReturnValue validateArguments = parser->CheckForRequiredArguments();

  if (validateArguments == itk::CommandLineArgumentParser::FAILED)
  {
    return EXIT_FAILURE;
  }
  else if (validateArguments == itk::CommandLineArgumentParser::HELPREQUESTED)
  {
    return EXIT_SUCCESS;
  }

  std::string testImageFileName;
  parser->GetCommandLineArgument("-test", testImageFileName);

  std::string baselineImageFileName;
  parser->GetCommandLineArgument("-base", baselineImageFileName);

  double diffThreshold = 0.0;
  parser->GetCommandLineArgument("-t", diffThreshold);

  unsigned long allowedTolerance = 0;
  parser->GetCommandLineArgument("-a", allowedTolerance);

  // Read images
  using ImageType = itk::Image<double, ITK_TEST_DIMENSION_MAX>;
  using ReaderType = itk::ImageFileReader<ImageType>;

  // Read the baseline file
  auto baselineReader = ReaderType::New();
  baselineReader->SetFileName(baselineImageFileName);
  try
  {
    baselineReader->Update();
  }
  catch (const itk::ExceptionObject & err)
  {
    std::cerr << "Error during reading baseline image: " << err << std::endl;
    return EXIT_FAILURE;
  }

  // Read the file to test
  auto testReader = ReaderType::New();
  testReader->SetFileName(testImageFileName);
  try
  {
    testReader->Update();
  }
  catch (const itk::ExceptionObject & err)
  {
    std::cerr << "Error during reading test image: " << err << std::endl;
    return EXIT_FAILURE;
  }

  // The sizes of the baseline and test image must match
  ImageType::SizeType baselineSize = baselineReader->GetOutput()->GetLargestPossibleRegion().GetSize();
  ImageType::SizeType testSize = testReader->GetOutput()->GetLargestPossibleRegion().GetSize();

  if (baselineSize != testSize)
  {
    std::cerr << "The size of the Baseline image and Test image do not match!" << std::endl;
    std::cerr << "Baseline image: " << baselineImageFileName << " has size " << baselineSize << std::endl;
    std::cerr << "Test image:     " << testImageFileName << " has size " << testSize << std::endl;
    return EXIT_FAILURE;
  }

  // Now compare the two images
  using ComparisonFilterType = itk::Testing::ComparisonImageFilter<ImageType, ImageType>;
  auto comparisonFilter = ComparisonFilterType::New();
  comparisonFilter->SetTestInput(testReader->GetOutput());
  comparisonFilter->SetValidInput(baselineReader->GetOutput());
  comparisonFilter->SetDifferenceThreshold(diffThreshold);
  try
  {
    comparisonFilter->Update();
  }
  catch (const itk::ExceptionObject & err)
  {
    std::cerr << "Error during comparing image: " << err << std::endl;
    return EXIT_FAILURE;
  }

  // itk::SizeValueType numberOfDifferentPixels = comparisonFilter->GetNumberOfPixelsWithDifferences(); // in ITK4
  unsigned long numberOfDifferentPixels = comparisonFilter->GetNumberOfPixelsWithDifferences();

  if (numberOfDifferentPixels > 0)
  {
    std::cerr << "There are " << numberOfDifferentPixels << " pixels with difference larger than " << diffThreshold
              << ", while " << allowedTolerance << " are allowed!" << std::endl;

    // Create name for diff image
    std::string diffImageFileName = itksys::SystemTools::GetFilenamePath(testImageFileName);
    diffImageFileName += "/";
    diffImageFileName += itksys::SystemTools::GetFilenameWithoutLastExtension(testImageFileName);
    diffImageFileName += "_DIFF";
    diffImageFileName += itksys::SystemTools::GetFilenameLastExtension(testImageFileName);

    try
    {
      itk::WriteImage(comparisonFilter->GetOutput(), diffImageFileName);
    }
    catch (const itk::ExceptionObject & err)
    {
      std::cerr << "Error during writing difference image: " << err << std::endl;
      return EXIT_FAILURE;
    }

    if (numberOfDifferentPixels > allowedTolerance)
    {
      return EXIT_FAILURE;
    }

  } // end if discrepancies

  return EXIT_SUCCESS;

} // end main
