#include "antsCommandLineParser.h"
#include "antsUtilities.h"
#include "ReadWriteData.h"

#include <algorithm>

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"

#include "itkCastImageFilter.h"
#include "itkConstantPadImageFilter.h"
#include "itkExtractImageFilter.h"
#include "itkFlipImageFilter.h"
#include "itkImageDuplicator.h"
#include "itkImageRegionIterator.h"
#include "itkIntensityWindowingImageFilter.h"
#include "itkImageRegionConstIteratorWithIndex.h"
#include "itkLabelStatisticsImageFilter.h"
#include "itkPermuteAxesImageFilter.h"
#include "itkStatisticsImageFilter.h"
#include "itkTileImageFilter.h"

namespace ants
{
int
CreateMosaic(itk::ants::CommandLineParser * parser)
{
  constexpr unsigned int ImageDimension = 3;

  using RealType = float;

  using PixelType = RealType;
  using RgbComponentType = unsigned char;
  using ScalarComponentType = unsigned char;
  using RgbPixelType = itk::RGBPixel<RgbComponentType>;

  using ImageType = itk::Image<PixelType, ImageDimension>;
  using SliceType = itk::Image<ScalarComponentType, ImageDimension - 1>;
  using RgbSliceType = itk::Image<RgbPixelType, ImageDimension - 1>;

  using RgbImageType = itk::Image<RgbPixelType, ImageDimension>;

  // Read in input image

  ImageType::Pointer inputImage = nullptr;

  itk::ants::CommandLineParser::OptionType::Pointer inputImageOption = parser->GetOption("input-image");
  if (inputImageOption && inputImageOption->GetNumberOfFunctions())
  {
    std::string inputFile = inputImageOption->GetFunction(0)->GetName();
    ReadImage<ImageType>(inputImage, inputFile.c_str());
  }
  else
  {
    std::cout << "Input image not specified." << std::endl;
    return EXIT_FAILURE;
  }
  ImageType::SizeType size = inputImage->GetRequestedRegion().GetSize();

  // Read in optional mask image

  ImageType::Pointer    maskImage = nullptr;
  ImageType::RegionType maskRegion;

  itk::ants::CommandLineParser::OptionType::Pointer maskImageOption = parser->GetOption("mask-image");
  if (maskImageOption && maskImageOption->GetNumberOfFunctions())
  {
    std::string maskFile = maskImageOption->GetFunction(0)->GetName();
    ReadImage<ImageType>(maskImage, maskFile.c_str());

    using ShortImageType = itk::Image<unsigned short, ImageDimension>;
    using CasterType = itk::CastImageFilter<ImageType, ShortImageType>;
    CasterType::Pointer caster = CasterType::New();
    caster->SetInput(maskImage);
    caster->Update();

    using StatsFilterType = itk::LabelStatisticsImageFilter<ShortImageType, ShortImageType>;
    StatsFilterType::Pointer stats = StatsFilterType::New();
    stats->SetLabelInput(caster->GetOutput());
    stats->SetInput(caster->GetOutput());
    stats->Update();

    maskRegion = stats->GetRegion(1);
  }

  // Read in optional Rgb image

  RgbImageType::Pointer rgbImage = nullptr;

  itk::ants::CommandLineParser::OptionType::Pointer rgbImageOption = parser->GetOption("rgb-image");
  if (rgbImageOption && rgbImageOption->GetNumberOfFunctions())
  {
    std::string rgbFile = rgbImageOption->GetFunction(0)->GetName();
    ReadImage<RgbImageType>(rgbImage, rgbFile.c_str());
  }

  RealType minIntensityValue = 0.0;
  RealType maxIntensityValue = 1.0;

  using StatisticsImageFilterType = itk::StatisticsImageFilter<ImageType>;
  StatisticsImageFilterType::Pointer statisticsImageFilter = StatisticsImageFilterType::New();
  statisticsImageFilter->SetInput(inputImage);
  statisticsImageFilter->Update();

  minIntensityValue = statisticsImageFilter->GetMinimum();
  maxIntensityValue = statisticsImageFilter->GetMaximum();

  // Rescale the input image to the range 0-255. Without an overlay, we write these values directly
  // as unsigned char for compatibility with different image formats.
  // With overlay(s), we need the scalar to be in the range 0-255 for the combined RGB pixel computation
  using IntensityWindowingImageFilterType = itk::IntensityWindowingImageFilter<ImageType, ImageType>;

  auto windowingFilter = IntensityWindowingImageFilterType::New();
  windowingFilter->SetInput(inputImage);
  windowingFilter->SetWindowMinimum(minIntensityValue);
  windowingFilter->SetWindowMaximum(maxIntensityValue);
  windowingFilter->SetOutputMinimum(0.0);
  windowingFilter->SetOutputMaximum(255.0);
  windowingFilter->Update();

  RealType alpha = 1.0;

  itk::ants::CommandLineParser::OptionType::Pointer alphaOption = parser->GetOption("alpha");
  if (alphaOption && alphaOption->GetNumberOfFunctions())
  {
    alpha = parser->Convert<RealType>(alphaOption->GetFunction(0)->GetName());

    if (alpha < itk::NumericTraits<RealType>::ZeroValue() || alpha > itk::NumericTraits<RealType>::OneValue())
    {
      std::cerr << "The alpha parameter must be between 0 and 1." << std::endl;
      return EXIT_FAILURE;
    }
  }

  // Add the functional overlays

  std::vector<RgbImageType::Pointer> functionalRgbImages;
  std::vector<ImageType::Pointer>    functionalMaskImages;
  std::vector<RealType>              functionalAlphaValues;

  if (rgbImage)
  {
    functionalRgbImages.push_back(rgbImage);
    functionalAlphaValues.push_back(alpha);
    if (maskImage.IsNull())
    {
      maskImage = ImageType::New();
      maskImage->CopyInformation(rgbImage);
      maskImage->SetRegions(rgbImage->GetRequestedRegion());
      maskImage->Allocate();
      maskImage->FillBuffer(itk::NumericTraits<typename ImageType::PixelType>::OneValue());

      using ShortImageType = itk::Image<unsigned short, ImageDimension>;
      using CasterType = itk::CastImageFilter<ImageType, ShortImageType>;
      CasterType::Pointer caster = CasterType::New();
      caster->SetInput(maskImage);
      caster->Update();

      using StatsFilterType = itk::LabelStatisticsImageFilter<ShortImageType, ShortImageType>;
      StatsFilterType::Pointer stats = StatsFilterType::New();
      stats->SetLabelInput(caster->GetOutput());
      stats->SetInput(caster->GetOutput());
      stats->Update();

      maskRegion = stats->GetRegion(1);
    }
    functionalMaskImages.push_back(maskImage);
  }

  itk::ants::CommandLineParser::OptionType::Pointer functionalOverlayOption = parser->GetOption("functional-overlay");
  if (functionalOverlayOption && functionalOverlayOption->GetNumberOfFunctions())
  {
    for (unsigned int n = 0; n < functionalOverlayOption->GetNumberOfFunctions(); n++)
    {
      if (functionalOverlayOption->GetFunction(n)->GetNumberOfParameters() < 2)
      {
        std::cerr << "Error:  each functional overlay must have an RGB image and mask."
                  << "See help menu." << std::endl;
        return EXIT_FAILURE;
      }

      // read RGB image

      std::string rgbFileName = functionalOverlayOption->GetFunction(n)->GetParameter(0);

      using RgbReaderType = itk::ImageFileReader<RgbImageType>;
      RgbReaderType::Pointer rgbReader = RgbReaderType::New();
      rgbReader->SetFileName(rgbFileName.c_str());
      try
      {
        rgbReader->Update();
      }
      catch (...)
      {
        std::cerr << "Error reading RGB file " << rgbFileName << std::endl;
        return EXIT_FAILURE;
      }
      functionalRgbImages.emplace_back(rgbReader->GetOutput());

      // read mask

      std::string maskFileName = functionalOverlayOption->GetFunction(n)->GetParameter(1);

      using MaskReaderType = itk::ImageFileReader<ImageType>;
      MaskReaderType::Pointer maskReader = MaskReaderType::New();
      maskReader->SetFileName(maskFileName.c_str());
      try
      {
        maskReader->Update();
      }
      catch (...)
      {
        std::cerr << "Error reading mask file " << maskFileName << std::endl;
        return EXIT_FAILURE;
      }
      functionalMaskImages.emplace_back(maskReader->GetOutput());

      if (functionalOverlayOption->GetFunction(n)->GetNumberOfParameters() > 2)
      {
        auto localAlpha = parser->Convert<RealType>(functionalOverlayOption->GetFunction(n)->GetParameter(2));
        functionalAlphaValues.push_back(localAlpha);
      }
      else
      {
        functionalAlphaValues.push_back(1.0);
      }
    }
  }

  // Get direction.  If not specified, pick direction with coarsest spacing.

  unsigned int direction = 0;

  itk::ants::CommandLineParser::OptionType::Pointer directionOption = parser->GetOption("direction");
  if (directionOption && directionOption->GetNumberOfFunctions())
  {
    std::string directionString = directionOption->GetFunction(0)->GetName();

    int physicalCoordinateComponent = -1;

    if (std::strcmp(directionString.c_str(), "0") == 0)
    {
      direction = 0;
    }
    else if (std::strcmp(directionString.c_str(), "1") == 0)
    {
      direction = 1;
    }
    else if (std::strcmp(directionString.c_str(), "2") == 0)
    {
      direction = 2;
    }
    else if (std::strcmp(directionString.c_str(), "x") == 0)
    {
      physicalCoordinateComponent = 0;
    }
    else if (std::strcmp(directionString.c_str(), "y") == 0)
    {
      physicalCoordinateComponent = 1;
    }
    else if (std::strcmp(directionString.c_str(), "z") == 0)
    {
      physicalCoordinateComponent = 2;
    }
    else
    {
      std::cerr << "Unrecognized direction option.  See help menu" << std::endl;
      return EXIT_FAILURE;
    }

    if (physicalCoordinateComponent >= 0)
    {
      float maxComponentValue = 0.0;

      ImageType::IndexType index;
      index.Fill(0);
      ImageType::PointType pointOrigin;
      inputImage->TransformIndexToPhysicalPoint(index, pointOrigin);

      for (unsigned int d = 0; d < ImageDimension; d++)
      {
        ImageType::PointType point;
        index.Fill(0);
        index[d] = 1;
        inputImage->TransformIndexToPhysicalPoint(index, point);

        ImageType::PointType::VectorType directionalVector = point - pointOrigin;

        if (itk::Math::abs(directionalVector[physicalCoordinateComponent]) > static_cast<double>(maxComponentValue))
        {
          direction = d;
        }
      }
    }
  }

  // Get padding/cropping options.

  int      paddingType = 0;
  RealType padValue = 0;

  itk::SizeValueType lowerBound[ImageDimension];
  itk::SizeValueType upperBound[ImageDimension];

  SliceType::RegionType            croppedSliceRegion;
  SliceType::RegionType::SizeType  croppedSliceSize;
  SliceType::RegionType::IndexType croppedSliceIndex;

  itk::ants::CommandLineParser::OptionType::Pointer paddingOption = parser->GetOption("pad-or-crop");
  if (paddingOption && paddingOption->GetNumberOfFunctions())
  {
    if (paddingOption->GetFunction(0)->GetNumberOfParameters() == 3)
    {
      std::vector<int> lowerBoundVector = parser->ConvertVector<int>(paddingOption->GetFunction(0)->GetParameter(0));
      std::vector<int> upperBoundVector = parser->ConvertVector<int>(paddingOption->GetFunction(0)->GetParameter(1));

      if (lowerBoundVector.size() != 2 || upperBoundVector.size() != 2)
      {
        std::cerr << "Incorrect padding specification." << std::endl;
        return EXIT_FAILURE;
      }
      int lowerBoundProduct = lowerBoundVector[0] * lowerBoundVector[1];
      int upperBoundProduct = upperBoundVector[0] * upperBoundVector[1];

      if (lowerBoundProduct < 0 || upperBoundProduct < 0 || upperBoundProduct * lowerBoundProduct < 0)
      {
        std::cerr << "Current capabilities do not include mixing of cropping and padding,"
                  << " i.e. negative and positive pad values, respectively" << std::endl;
        return EXIT_FAILURE;
      }

      if (lowerBoundVector[0] < 0)
      {
        paddingType = -1;
        unsigned int count = 0;
        for (unsigned int d = 0; d < ImageDimension; d++)
        {
          if (d != direction)
          {
            croppedSliceSize[count] = std::min(
                size[d] - (itk::Math::abs(lowerBoundVector[count]) + itk::Math::abs(upperBoundVector[count])),
                size[d]);

            croppedSliceIndex[count] = itk::Math::abs(lowerBoundVector[count]);
            count++;
          }
        }
        croppedSliceRegion.SetSize(croppedSliceSize);
        croppedSliceRegion.SetIndex(croppedSliceIndex);
      }
      else
      {
        paddingType = 1;
        for (unsigned int d = 0; d < ImageDimension - 1; d++)
        {
          lowerBound[d] = lowerBoundVector[d];
          upperBound[d] = upperBoundVector[d];
        }
      }
    }
    else
    {
      int         padWidth = 0;
      std::string padWidthString;
      if (paddingOption->GetFunction(0)->GetNumberOfParameters() == 0)
      {
        padWidthString = paddingOption->GetFunction(0)->GetName();
      }
      else if (paddingOption->GetFunction(0)->GetNumberOfParameters() <= 2)
      {
        padWidthString = paddingOption->GetFunction(0)->GetParameter(0);
        padValue = parser->Convert<int>(paddingOption->GetFunction(0)->GetParameter(1));
      }

      if (padWidthString.find(std::string("mask")) != std::string::npos)
      {
        if (!maskImage)
        {
          std::cerr << "Mask image is not specified." << std::endl;
          return EXIT_FAILURE;
        }

        int offset = 0;
        if (padWidthString.find(std::string("+")) != std::string::npos)
        {
          std::string offsetString = padWidthString.substr(padWidthString.find(std::string("+")) + 1);
          offset = parser->Convert<int>(offsetString);
        }
        if (padWidthString.find(std::string("-")) != std::string::npos)
        {
          std::string offsetString = padWidthString.substr(padWidthString.find(std::string("-")) + 1);
          offset = parser->Convert<int>(offsetString);
          offset *= -1;
        }

        paddingType = -1;
        unsigned int count = 0;
        for (unsigned int d = 0; d < ImageDimension; d++)
        {
          if (d != direction)
          {
            croppedSliceSize[count] = std::min(maskRegion.GetSize()[d] + 2 * offset, size[d]);
            croppedSliceIndex[count] = maskRegion.GetIndex()[d] - offset;
            count++;
          }
        }
        croppedSliceRegion.SetSize(croppedSliceSize);
        croppedSliceRegion.SetIndex(croppedSliceIndex);
      }
      else
      {
        padWidth = parser->Convert<int>(padWidthString);

        if (padWidth < 0)
        {
          paddingType = -1;
          unsigned int count = 0;
          for (unsigned int d = 0; d < ImageDimension; d++)
          {
            if (d != direction)
            {
              croppedSliceSize[count] = std::min(size[d] - 2 * itk::Math::abs(padWidth), size[d]);
              croppedSliceIndex[count] = itk::Math::abs(padWidth);
              count++;
            }
          }
          croppedSliceRegion.SetSize(croppedSliceSize);
          croppedSliceRegion.SetIndex(croppedSliceIndex);
        }
        else
        {
          paddingType = 1;
          for (unsigned int d = 0; d < ImageDimension - 1; d++)
          {
            lowerBound[d] = padWidth;
            upperBound[d] = padWidth;
          }
        }
      }
    }
  }

  // Get the slices

  std::vector<unsigned int> whichSlices;
  for (unsigned int n = 0; n < size[direction]; n++)
  {
    whichSlices.push_back(n);
  }

  itk::ants::CommandLineParser::OptionType::Pointer slicesOption = parser->GetOption("slices");
  if (slicesOption && slicesOption->GetNumberOfFunctions())
  {
    int numberOfSlicesToIncrement = 1;
    int startingSlice = 0;
    int endSlice = size[direction] - 1;

    bool readSlices = false;
    bool reverseOrder = false;

    if (slicesOption->GetFunction(0)->GetNumberOfParameters() == 0)
    {
      std::vector<int> slicesVector = parser->ConvertVector<int>(slicesOption->GetFunction(0)->GetName());
      if (slicesVector.size() == 1)
      {
        numberOfSlicesToIncrement = slicesVector[0];
        if (numberOfSlicesToIncrement < 0)
        {
          reverseOrder = true;
        }
      }
      else
      {
        whichSlices = parser->ConvertVector<unsigned int>(slicesOption->GetFunction(0)->GetName());
        readSlices = true;
      }
    }

    if (!readSlices)
    {
      if (slicesOption->GetFunction(0)->GetNumberOfParameters() > 0)
      {
        numberOfSlicesToIncrement = parser->Convert<int>(slicesOption->GetFunction(0)->GetParameter(0));
        if (numberOfSlicesToIncrement < 0)
        {
          reverseOrder = true;
        }
      }
      if (numberOfSlicesToIncrement == 0)
      {
        std::cerr << "Need greater than 0 slices for incrementing." << std::endl;
        return EXIT_FAILURE;
      }

      std::ostringstream stream;
      stream << startingSlice;
      std::string startingSliceString = stream.str();
      stream << endSlice;
      std::string endSliceString = stream.str();

      if (slicesOption->GetFunction(0)->GetNumberOfParameters() > 1)
      {
        startingSliceString = slicesOption->GetFunction(0)->GetParameter(1);
      }
      if (slicesOption->GetFunction(0)->GetNumberOfParameters() > 2)
      {
        endSliceString = slicesOption->GetFunction(0)->GetParameter(2);
      }

      bool isStartingSliceMaskDependent = startingSliceString.find(std::string("mask")) != std::string::npos;
      bool isEndSliceMaskDependent = endSliceString.find(std::string("mask")) != std::string::npos;

      if (isStartingSliceMaskDependent || isEndSliceMaskDependent)
      {
        if (!maskImage)
        {
          std::cerr << "Mask image is not specified." << std::endl;
          return EXIT_FAILURE;
        }

        if (isStartingSliceMaskDependent)
        {
          startingSlice = maskRegion.GetIndex()[direction];
        }
        else
        {
          startingSlice = parser->Convert<unsigned int>(startingSliceString);
        }

        if (startingSliceString.find(std::string("+")) != std::string::npos)
        {
          std::string offsetString = startingSliceString.substr(startingSliceString.find(std::string("+")) + 1);
          int         offset = parser->Convert<int>(offsetString);
          startingSlice += offset;
        }
        else if (startingSliceString.find(std::string("-")) != std::string::npos)
        {
          std::string offsetString = startingSliceString.substr(startingSliceString.find(std::string("-")) + 1);
          int         offset = parser->Convert<int>(offsetString);
          startingSlice -= offset;
        }

        if (isEndSliceMaskDependent)
        {
          endSlice = maskRegion.GetIndex()[direction] + maskRegion.GetSize()[direction];
        }
        else
        {
          endSlice = parser->Convert<unsigned int>(endSliceString);
        }

        if (endSliceString.find(std::string("+")) != std::string::npos)
        {
          std::string offsetString = endSliceString.substr(endSliceString.find(std::string("+")) + 1);
          int         offset = parser->Convert<int>(offsetString);
          endSlice += offset;
        }
        else if (endSliceString.find(std::string("-")) != std::string::npos)
        {
          std::string offsetString = endSliceString.substr(endSliceString.find(std::string("-")) + 1);
          int         offset = parser->Convert<int>(offsetString);
          endSlice -= offset;
        }
      }
      else
      {
        startingSlice = parser->Convert<unsigned int>(startingSliceString);
        endSlice = parser->Convert<unsigned int>(endSliceString);
      }

      startingSlice = std::max(itk::NumericTraits<int>::ZeroValue(), startingSlice);
      startingSlice = std::min(startingSlice, static_cast<int>(size[direction] - 1));

      endSlice = std::max(itk::NumericTraits<int>::ZeroValue(), endSlice);
      endSlice = std::min(endSlice, static_cast<int>(size[direction] - 1));

      whichSlices.clear();
      if (reverseOrder)
      {
        for (int n = endSlice; n >= startingSlice; n -= itk::Math::abs(numberOfSlicesToIncrement))
        {
          whichSlices.push_back(n);
        }
      }
      else
      {
        for (int n = startingSlice; n <= endSlice; n += numberOfSlicesToIncrement)
        {
          whichSlices.push_back(n);
        }
      }
    }
  }

  // Get tile geometry.

  unsigned long numberOfSlices = whichSlices.size();

  int numberOfRows = 0;
  int numberOfColumns = 0;

  itk::ants::CommandLineParser::OptionType::Pointer tileGeometryOption = parser->GetOption("tile-geometry");
  if (tileGeometryOption && tileGeometryOption->GetNumberOfFunctions())
  {
    std::vector<int> layout = parser->ConvertVector<int>(tileGeometryOption->GetFunction(0)->GetName());
    if (layout.size() > 2)
    {
      std::cerr << "Tile geometry is specified as numberOfRowsxnumberOfColumns" << std::endl;
      return EXIT_FAILURE;
    }
    numberOfRows = std::min(static_cast<int>(layout[0]), static_cast<int>(numberOfSlices));
    numberOfColumns = std::min(static_cast<int>(layout[1]), static_cast<int>(numberOfSlices));
  }

  if (numberOfRows <= 0 && numberOfColumns > 0)
  {
    numberOfRows = std::ceil(static_cast<float>(numberOfSlices) / static_cast<float>(numberOfColumns));
  }
  else if (numberOfColumns <= 0 && numberOfRows > 0)
  {
    numberOfColumns = std::ceil(static_cast<float>(numberOfSlices) / static_cast<float>(numberOfRows));
  }
  else if (numberOfColumns <= 0 && numberOfRows <= 0)
  {
    numberOfRows = static_cast<int>(std::sqrt(static_cast<float>(numberOfSlices)));
    numberOfColumns = std::ceil(static_cast<float>(numberOfSlices) / static_cast<float>(numberOfRows));
  }

  itk::ants::CommandLineParser::OptionType::Pointer flipOption = parser->GetOption("flip-slice");

  bool doFlipHorizontally = false;
  bool doFlipVertically = false;

  if (flipOption && flipOption->GetNumberOfFunctions())
  {
    std::vector<bool> layout = parser->ConvertVector<bool>(flipOption->GetFunction(0)->GetName());
    if (layout.size() > 2)
    {
      std::cerr << "Flip layout is specified as doFlipXxdoFlipY" << std::endl;
      return EXIT_FAILURE;
    }
    doFlipHorizontally = layout[0];
    doFlipVertically = layout[1];
  }

  itk::ants::CommandLineParser::OptionType::Pointer permuteOption = parser->GetOption("permute-axes");

  bool doPermute = false;

  if (permuteOption && permuteOption->GetNumberOfFunctions())
  {
    doPermute = parser->Convert<bool>(permuteOption->GetFunction(0)->GetName());
  }

  // Now do the tiling

  std::cout << "Slices[" << direction << "]: " << whichSlices.size() << std::endl;
  std::cout << "Rows:  " << numberOfRows << std::endl;
  std::cout << "Columns:  " << numberOfColumns << std::endl;


  using TileFilterType = itk::TileImageFilter<SliceType, SliceType>;
  TileFilterType::LayoutArrayType array;

  array[0] = numberOfColumns;
  array[1] = numberOfRows;

  ImageType::RegionType region;
  size[direction] = 0;

  TileFilterType::Pointer tileFilter = TileFilterType::New();
  tileFilter->SetLayout(array);

  using RgbTileFilterType = itk::TileImageFilter<RgbSliceType, RgbSliceType>;
  RgbTileFilterType::Pointer rgbTileFilter = RgbTileFilterType::New();
  rgbTileFilter->SetLayout(array);

  for (unsigned int i = 0; i < whichSlices.size(); i++)
  {
    unsigned int whichSlice = whichSlices[i];

    std::cout << "Processing slice " << whichSlice << std::endl;

    ImageType::IndexType index;
    index.Fill(0);
    index[direction] = static_cast<int>(whichSlice);
    region.SetIndex(index);
    region.SetSize(size);

    using ExtracterType = itk::ExtractImageFilter<ImageType, SliceType>;
    ExtracterType::Pointer extracter = ExtracterType::New();
    extracter->SetInput(windowingFilter->GetOutput());
    extracter->SetExtractionRegion(region);
    extracter->SetDirectionCollapseToIdentity();

    SliceType::Pointer outputSlice = nullptr;
    SliceType::Pointer outputSlice2 = nullptr;

    if (paddingType == -1)
    {
      using ExtracterType2 = itk::ExtractImageFilter<SliceType, SliceType>;
      ExtracterType2::Pointer extracter2 = ExtracterType2::New();
      extracter2->SetInput(extracter->GetOutput());
      extracter2->SetExtractionRegion(croppedSliceRegion);
      extracter2->SetDirectionCollapseToIdentity();

      outputSlice = extracter2->GetOutput();
      outputSlice->Update();
      outputSlice->DisconnectPipeline();
    }
    else if (paddingType == 1)
    {
      using PadderType = itk::ConstantPadImageFilter<SliceType, SliceType>;
      PadderType::Pointer padder = PadderType::New();
      padder->SetInput(extracter->GetOutput());
      padder->SetPadLowerBound(lowerBound);
      padder->SetPadUpperBound(upperBound);
      padder->SetConstant(static_cast<PixelType>(padValue));

      outputSlice = padder->GetOutput();
      outputSlice->Update();
      outputSlice->DisconnectPipeline();
    }
    else // paddingType == 0
    {
      outputSlice = extracter->GetOutput();
      outputSlice->Update();
      outputSlice->DisconnectPipeline();
    }

    using FlipFilterType = itk::FlipImageFilter<SliceType>;
    FlipFilterType::Pointer           flipper = FlipFilterType::New();
    FlipFilterType::FlipAxesArrayType flipArray;
    flipArray[0] = doFlipHorizontally;
    flipArray[1] = doFlipVertically;

    flipper->SetInput(outputSlice);
    flipper->SetFlipAxes(flipArray);

    using PermuteAxesImageFilterType = itk::PermuteAxesImageFilter<SliceType>;
    itk::FixedArray<unsigned int, 2> order;
    order[0] = 0;
    order[1] = 1;
    if (doPermute)
    {
      order[0] = 1;
      order[1] = 0;
    }
    PermuteAxesImageFilterType::Pointer permuteAxesFilter = PermuteAxesImageFilterType::New();
    permuteAxesFilter->SetInput(flipper->GetOutput());
    permuteAxesFilter->SetOrder(order);

    outputSlice2 = permuteAxesFilter->GetOutput();
    outputSlice2->Update();
    outputSlice2->DisconnectPipeline();

    if (!functionalRgbImages.empty())
    {
      RgbSliceType::Pointer compositeRgbSlice = nullptr;
      RealType              compositeAlpha = 1.0;

      for (unsigned int n = 0; n < functionalRgbImages.size(); n++)
      {
        SliceType::Pointer outputMaskSlice = nullptr;
        SliceType::Pointer outputMaskSlice2 = nullptr;

        ExtracterType::Pointer maskExtracter = ExtracterType::New();
        maskExtracter->SetInput(functionalMaskImages[n]);
        maskExtracter->SetExtractionRegion(region);
        maskExtracter->SetDirectionCollapseToIdentity();

        if (paddingType == -1)
        {
          using ExtracterType2 = itk::ExtractImageFilter<SliceType, SliceType>;
          ExtracterType2::Pointer maskExtracter2 = ExtracterType2::New();
          maskExtracter2->SetInput(maskExtracter->GetOutput());
          maskExtracter2->SetExtractionRegion(croppedSliceRegion);
          maskExtracter2->SetDirectionCollapseToIdentity();

          outputMaskSlice = maskExtracter2->GetOutput();
          outputMaskSlice->Update();
          outputMaskSlice->DisconnectPipeline();
        }
        else if (paddingType == 1)
        {
          using PadderType = itk::ConstantPadImageFilter<SliceType, SliceType>;
          PadderType::Pointer maskPadder = PadderType::New();
          maskPadder->SetInput(maskExtracter->GetOutput());
          maskPadder->SetPadLowerBound(lowerBound);
          maskPadder->SetPadUpperBound(upperBound);
          maskPadder->SetConstant(0);

          outputMaskSlice = maskPadder->GetOutput();
          outputMaskSlice->Update();
          outputMaskSlice->DisconnectPipeline();
        }
        else // paddingType == 0
        {
          outputMaskSlice = maskExtracter->GetOutput();
          outputMaskSlice->Update();
          outputMaskSlice->DisconnectPipeline();
        }

        FlipFilterType::Pointer maskFlipper = FlipFilterType::New();
        maskFlipper->SetInput(outputMaskSlice);
        maskFlipper->SetFlipAxes(flipArray);

        PermuteAxesImageFilterType::Pointer maskPermuteAxesFilter = PermuteAxesImageFilterType::New();
        maskPermuteAxesFilter->SetInput(maskFlipper->GetOutput());
        maskPermuteAxesFilter->SetOrder(order);

        outputMaskSlice2 = maskPermuteAxesFilter->GetOutput();
        outputMaskSlice2->Update();
        outputMaskSlice2->DisconnectPipeline();

        using RgbExtracterType = itk::ExtractImageFilter<RgbImageType, RgbSliceType>;
        RgbExtracterType::Pointer rgbExtracter = RgbExtracterType::New();
        rgbExtracter->SetInput(functionalRgbImages[n]);
        rgbExtracter->SetExtractionRegion(region);
        rgbExtracter->SetDirectionCollapseToIdentity();

        RgbSliceType::Pointer outputRgbSlice = nullptr;
        RgbSliceType::Pointer outputRgbSlice2 = nullptr;

        if (paddingType == -1)
        {
          using RgbExtracterType2 = itk::ExtractImageFilter<RgbSliceType, RgbSliceType>;
          RgbExtracterType2::Pointer rgbExtracter2 = RgbExtracterType2::New();
          rgbExtracter2->SetInput(rgbExtracter->GetOutput());
          rgbExtracter2->SetExtractionRegion(croppedSliceRegion);
          rgbExtracter2->SetDirectionCollapseToIdentity();

          outputRgbSlice = rgbExtracter2->GetOutput();
          outputRgbSlice->Update();
          outputRgbSlice->DisconnectPipeline();
        }
        else if (paddingType == 1)
        {
          using RgbPadderType = itk::ConstantPadImageFilter<RgbSliceType, RgbSliceType>;
          RgbPadderType::Pointer rgbPadder = RgbPadderType::New();
          rgbPadder->SetInput(rgbExtracter->GetOutput());
          rgbPadder->SetPadLowerBound(lowerBound);
          rgbPadder->SetPadUpperBound(upperBound);
          RgbPixelType rgbPadValue;
          rgbPadValue.Fill(padValue);
          rgbPadder->SetConstant(rgbPadValue);

          outputRgbSlice = rgbPadder->GetOutput();
          outputRgbSlice->Update();
          outputRgbSlice->DisconnectPipeline();
        }
        else // paddingType == 0
        {
          outputRgbSlice = rgbExtracter->GetOutput();
          outputRgbSlice->Update();
          outputRgbSlice->DisconnectPipeline();
        }

        using RgbFlipFilterType = itk::FlipImageFilter<RgbSliceType>;
        RgbFlipFilterType::Pointer           rgbFlipper = RgbFlipFilterType::New();
        RgbFlipFilterType::FlipAxesArrayType rgbFlipArray;
        rgbFlipArray[0] = doFlipHorizontally;
        rgbFlipArray[1] = doFlipVertically;

        rgbFlipper->SetInput(outputRgbSlice);
        rgbFlipper->SetFlipAxes(rgbFlipArray);

        using RgbPermuteAxesImageFilterType = itk::PermuteAxesImageFilter<RgbSliceType>;
        itk::FixedArray<unsigned int, 2> rgbOrder;
        rgbOrder[0] = 0;
        rgbOrder[1] = 1;
        if (doPermute)
        {
          rgbOrder[0] = 1;
          rgbOrder[1] = 0;
        }
        RgbPermuteAxesImageFilterType::Pointer rgbPermuteAxesFilter = RgbPermuteAxesImageFilterType::New();
        rgbPermuteAxesFilter->SetInput(rgbFlipper->GetOutput());
        rgbPermuteAxesFilter->SetOrder(rgbOrder);

        outputRgbSlice2 = rgbPermuteAxesFilter->GetOutput();
        outputRgbSlice2->Update();
        outputRgbSlice2->DisconnectPipeline();

        RealType functionalAlpha = functionalAlphaValues[n];
        RealType backgroundAlpha = compositeAlpha;
        RealType currentAlpha =
          itk::NumericTraits<RealType>::OneValue() - (itk::NumericTraits<RealType>::OneValue() - functionalAlpha) *
                                                       (itk::NumericTraits<RealType>::OneValue() - backgroundAlpha);

        // combine grayscale slice and rgb slice
        itk::ImageRegionConstIteratorWithIndex<SliceType> It(outputSlice2, outputSlice2->GetRequestedRegion());
        itk::ImageRegionIterator<RgbSliceType>            ItRgb(outputRgbSlice2, outputRgbSlice2->GetRequestedRegion());
        for (It.GoToBegin(), ItRgb.GoToBegin(); !It.IsAtEnd(); ++It, ++ItRgb)
        {
          RgbPixelType rgbPixel = ItRgb.Get();

          if (n == 0)
          {
            RealType pixel = static_cast<RealType>(It.Get());

            if (outputMaskSlice2 && !itk::Math::FloatAlmostEqual(
                static_cast<RealType>(outputMaskSlice2->GetPixel(It.GetIndex())),
                itk::NumericTraits<PixelType>::ZeroValue()))
            {
              rgbPixel.SetRed(
                static_cast<RgbComponentType>((itk::NumericTraits<RealType>::OneValue() - functionalAlpha) * pixel +
                                              functionalAlpha * rgbPixel.GetRed()));
              rgbPixel.SetGreen(
                static_cast<RgbComponentType>((itk::NumericTraits<RealType>::OneValue() - functionalAlpha) * pixel +
                                              functionalAlpha * rgbPixel.GetGreen()));
              rgbPixel.SetBlue(
                static_cast<RgbComponentType>((itk::NumericTraits<RealType>::OneValue() - functionalAlpha) * pixel +
                                              functionalAlpha * rgbPixel.GetBlue()));
            }
            else
            {
              rgbPixel.SetRed(pixel);
              rgbPixel.SetGreen(pixel);
              rgbPixel.SetBlue(pixel);
            }
            ItRgb.Set(rgbPixel);
          }
          else
          {
            // http://stackoverflow.com/questions/726549/algorithm-for-additive-color-mixing-for-rgb-values
            // or
            // http://en.wikipedia.org/wiki/Alpha_compositing

            if (outputMaskSlice2 && !itk::Math::FloatAlmostEqual(
                static_cast<RealType>(outputMaskSlice2->GetPixel(It.GetIndex())),
                itk::NumericTraits<RealType>::ZeroValue()))
            {
              RealType functionalRed = rgbPixel.GetRed() / static_cast<RealType>(255.0);
              RealType functionalGreen = rgbPixel.GetGreen() / static_cast<RealType>(255.0);
              RealType functionalBlue = rgbPixel.GetBlue() / static_cast<RealType>(255.0);

              RgbPixelType backgroundRgbPixel = compositeRgbSlice->GetPixel(It.GetIndex());

              RealType backgroundRed = backgroundRgbPixel.GetRed() / static_cast<RealType>(255.0);
              RealType backgroundGreen = backgroundRgbPixel.GetGreen() / static_cast<RealType>(255.0);
              RealType backgroundBlue = backgroundRgbPixel.GetBlue() / static_cast<RealType>(255.0);

              RealType currentRed = functionalRed * functionalAlpha / currentAlpha +
                                    backgroundRed * backgroundAlpha *
                                      (itk::NumericTraits<RealType>::OneValue() - functionalAlpha) / currentAlpha;
              RealType currentGreen = functionalGreen * functionalAlpha / currentAlpha +
                                      backgroundGreen * backgroundAlpha *
                                        (itk::NumericTraits<RealType>::OneValue() - functionalAlpha) / currentAlpha;
              RealType currentBlue = functionalBlue * functionalAlpha / currentAlpha +
                                     backgroundBlue * backgroundAlpha *
                                       (itk::NumericTraits<RealType>::OneValue() - functionalAlpha) / currentAlpha;

              rgbPixel.SetRed(currentRed * static_cast<RealType>(255.0));
              rgbPixel.SetGreen(currentGreen * static_cast<RealType>(255.0));
              rgbPixel.SetBlue(currentBlue * static_cast<RealType>(255.0));

              compositeRgbSlice->SetPixel(It.GetIndex(), rgbPixel);
            }
          }
        }
        if (n == 0)
        {
          using DuplicatorType = itk::ImageDuplicator<RgbSliceType>;
          DuplicatorType::Pointer duplicator = DuplicatorType::New();
          duplicator->SetInputImage(outputRgbSlice2);
          duplicator->Update();

          compositeRgbSlice = duplicator->GetOutput();
        }
        compositeAlpha = currentAlpha;
      }
      rgbTileFilter->SetInput(i, compositeRgbSlice);
    }
    else
    {
      tileFilter->SetInput(i, outputSlice2);
    }
  }

  itk::ants::CommandLineParser::OptionType::Pointer outputOption = parser->GetOption("output");
  if (outputOption && outputOption->GetNumberOfFunctions())
  {
    std::string outputFile = outputOption->GetFunction(0)->GetName();
    if (!functionalRgbImages.empty())
    {
      rgbTileFilter->Update();
      ANTs::WriteImage<RgbSliceType>(rgbTileFilter->GetOutput(), outputFile.c_str());
    }
    else
    {
      tileFilter->Update();
      ANTs::WriteImage<SliceType>(tileFilter->GetOutput(), outputFile.c_str());
    }
  }
  else
  {
    std::cerr << "No output filename specified." << std::endl;
    return EXIT_FAILURE;
  }

  return EXIT_SUCCESS;
}

void
InitializeCommandLineOptions(itk::ants::CommandLineParser * parser)
{
  using OptionType = itk::ants::CommandLineParser::OptionType;

  {
    std::string description = std::string("Main input is a 3-D grayscale image.  ");

    OptionType::Pointer option = OptionType::New();
    option->SetLongName("input-image");
    option->SetShortName('i');
    option->SetUsageOption(0, "inputImageFilename");
    option->SetDescription(description);
    parser->AddOption(option);
  }

  {
    std::string description = std::string("An optional Rgb image can be added as an overlay.  ") +
                              std::string("It must have the same image geometry as the input ") +
                              std::string("grayscale image.");

    OptionType::Pointer option = OptionType::New();
    option->SetLongName("rgb-image");
    option->SetShortName('r');
    option->SetUsageOption(0, "rgbImageFilename");
    option->SetDescription(description);
    parser->AddOption(option);
  }

  {
    std::string description = std::string("Specifies the ROI of the RGB voxels used.  ");

    OptionType::Pointer option = OptionType::New();
    option->SetLongName("mask-image");
    option->SetShortName('x');
    option->SetUsageOption(0, "maskImageFilename");
    option->SetDescription(description);
    parser->AddOption(option);
  }

  {
    std::string description = std::string("If an Rgb image is provided, render the overlay using the specified ") +
                              std::string("alpha parameter.");

    OptionType::Pointer option = OptionType::New();
    option->SetLongName("alpha");
    option->SetShortName('a');
    option->SetUsageOption(0, "value");
    option->SetDescription(description);
    parser->AddOption(option);
  }

  {
    std::string description = std::string("A functional overlay can be specified using both ") +
                              std::string("and rgb image and a mask specifying where that ") +
                              std::string("rgb image should be applied.  Both images must ") +
                              std::string("have the same image geometry as the input image. ") +
                              std::string("Optionally, an alpha parameter can be specified.") +
                              std::string("Note that more than one functional overlays can ") +
                              std::string("be rendered, the order in which they are specified ") +
                              std::string("on the command line matters, and rgb images are ") +
                              std::string("assumed to be unsigned char [0,255].");

    OptionType::Pointer option = OptionType::New();
    option->SetLongName("functional-overlay");
    option->SetShortName('e');
    option->SetUsageOption(0, "[rgbImageFileName,maskImageFileName,<alpha=1>]");
    option->SetDescription(description);
    parser->AddOption(option);
  }

  {
    std::string description = std::string("The output is the tiled mosaic image.  Without an RGB overlay") +
                              std::string("we do not alter the intensity values of the input image.  ") +
                              std::string("Therefore, the output suffix needs to be associated with a ") +
                              std::string("format that supports float images (not .jpg or .png).  If ") +
                              std::string("one or more RGB overlays are supported then we rescale ") +
                              std::string("the input image intensities to also be in the range of [0,255] ") +
                              std::string("which permits a .png or .jpg output.");

    OptionType::Pointer option = OptionType::New();
    option->SetLongName("output");
    option->SetShortName('o');
    option->SetUsageOption(0, "tiledMosaicImage");
    option->SetDescription(description);
    parser->AddOption(option);
  }

  {
    std::string description = std::string("The tile geometry specifies the number of rows and columns ") +
                              std::string("in the output image.  For example, if the user specifies ") +
                              std::string("\'5x10\', then 5 rows by 10 columns of slices are rendered. ") +
                              std::string("If R < 0 and C > 0 (or vice versa), the negative value is ") +
                              std::string("selected based on direction.");

    OptionType::Pointer option = OptionType::New();
    option->SetLongName("tile-geometry");
    option->SetShortName('t');
    option->SetUsageOption(0, "RxC");
    option->SetDescription(description);
    parser->AddOption(option);
  }

  {
    std::string description =
      std::string("Specifies the direction of the slices.  This can be based on the how ") +
      std::string("the image is stored in memory or can be based on how the image is aligned ") +
      std::string("in physical space.  If no direction is specified, ") +
      std::string("the z-direction (axial?) is chosen.");

    OptionType::Pointer option = OptionType::New();
    option->SetLongName("direction");
    option->SetShortName('d');
    option->SetUsageOption(0, "0/1/2/x/y/(z)");
    option->SetDescription(description);
    parser->AddOption(option);
  }

  {
    std::string description = std::string("The user can specify whether to pad or crop a specified voxel-width ") +
                              std::string("boundary of each individual slice.  For this program, cropping is ") +
                              std::string("simply padding with negative voxel-widths.  If one pads (+), the ") +
                              std::string("user can also specify a constant pad value (default = 0). If a mask is ") +
                              std::string("specified, the user can use the mask to define the region, by using ") +
                              std::string(R"(the keyword "mask" plus an offset, e.g. "-p mask+3".)");

    OptionType::Pointer option = OptionType::New();
    option->SetLongName("pad-or-crop");
    option->SetShortName('p');
    option->SetUsageOption(0, "padVoxelWidth");
    option->SetUsageOption(1, "[padVoxelWidth,<constantValue=0>]");
    option->SetUsageOption(2, "[lowerPadding[0]xlowerPadding[1],upperPadding[0]xupperPadding[1],constantValue]");
    option->SetDescription(description);
    parser->AddOption(option);
  }

  {
    std::string description = std::string("This option gives the user more control over what slices ") +
                              std::string("to use for rendering.  The user can specify specific slices ") +
                              std::string("for a particular order.  Alternatively the user can specify ") +
                              std::string("the number slices to increment with the optional specification of ") +
                              std::string("which slices to start and end the sequence.  A negative value ") +
                              std::string("for the numberOfSlicesToIncrement causes rendering in the reverse ") +
                              std::string("order.  For the third option, minSlice < maxSlice.  If a mask is ") +
                              std::string("specified, the user can use the mask to define the region, by using ") +
                              std::string(R"(the keyword "mask" plus an offset, e.g. "-s [1,mask-3,200]".)") +
                              std::string("For the third option, minSlice < maxSlice.");

    OptionType::Pointer option = OptionType::New();
    option->SetLongName("slices");
    option->SetShortName('s');
    option->SetUsageOption(0, "Slice1xSlice2xSlice3...");
    option->SetUsageOption(1, "numberOfSlicesToIncrement");
    option->SetUsageOption(2, "[numberOfSlicesToIncrement,<minSlice=0>,<maxSlice=lastSlice>]");
    option->SetDescription(description);
    parser->AddOption(option);
  }

  {
    std::string description = std::string("Flip individual slice images horizontally and/or vertically, specified ") +
                              std::string(R"(e.g. as '0x1' or '1x1'.)");

    OptionType::Pointer option = OptionType::New();
    option->SetLongName("flip-slice");
    option->SetShortName('f');
    option->SetUsageOption(0, "flipXxflipY");
    option->SetDescription(description);
    parser->AddOption(option);
  }

  {
    std::string description = std::string("Permute (or swap) the axes of the individual slice images.");

    OptionType::Pointer option = OptionType::New();
    option->SetLongName("permute-axes");
    option->SetShortName('g');
    option->SetUsageOption(0, "doPermute");
    option->SetDescription(description);
    parser->AddOption(option);
  }

  {
    std::string description = std::string("Print the help menu (short version).");

    OptionType::Pointer option = OptionType::New();
    option->SetShortName('h');
    option->SetDescription(description);
    parser->AddOption(option);
  }

  {
    std::string description = std::string("Print the help menu.");

    OptionType::Pointer option = OptionType::New();
    option->SetLongName("help");
    option->SetDescription(description);
    parser->AddOption(option);
  }
}

// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int
CreateTiledMosaic(std::vector<std::string> args, std::ostream * /*out_stream = nullptr */)
{
  // put the arguments coming in as 'args' into standard (argc,argv) format;
  // 'args' doesn't have the command name as first, argument, so add it manually;
  // 'args' may have adjacent arguments concatenated into one argument,
  // which the parser should handle
  args.insert(args.begin(), "CreateTiledMosaic");

  int     argc = args.size();
  char ** argv = new char *[args.size() + 1];
  for (unsigned int i = 0; i < args.size(); ++i)
  {
    // allocate space for the string plus a null character
    argv[i] = new char[args[i].length() + 1];
    std::strncpy(argv[i], args[i].c_str(), args[i].length());
    // place the null character in the end
    argv[i][args[i].length()] = '\0';
  }
  argv[argc] = nullptr;
  // class to automatically cleanup argv upon destruction
  class Cleanup_argv
  {
  public:
    Cleanup_argv(char ** argv_, int argc_plus_one_)
      : argv(argv_)
      , argc_plus_one(argc_plus_one_)
    {}

    ~Cleanup_argv()
    {
      for (unsigned int i = 0; i < argc_plus_one; ++i)
      {
        delete[] argv[i];
      }
      delete[] argv;
    }

  private:
    char **      argv;
    unsigned int argc_plus_one;
  };
  Cleanup_argv cleanup_argv(argv, argc + 1);

  // antscout->set_stream( out_stream );


  itk::ants::CommandLineParser::Pointer parser = itk::ants::CommandLineParser::New();

  parser->SetCommand(argv[0]);

  std::string commandDescription = std::string("Render a 3-D image volume with optional Rgb overlay.");

  parser->SetCommandDescription(commandDescription);
  InitializeCommandLineOptions(parser);

  if (parser->Parse(argc, argv) == EXIT_FAILURE)
  {
    return EXIT_FAILURE;
  }

  if (argc == 1)
  {
    parser->PrintMenu(std::cout, 5, false);
    return EXIT_FAILURE;
  }
  else if (parser->GetOption("help")->GetFunction() &&
           parser->Convert<bool>(parser->GetOption("help")->GetFunction()->GetName()))
  {
    parser->PrintMenu(std::cout, 5, false);
    return EXIT_SUCCESS;
  }
  else if (parser->GetOption('h')->GetFunction() &&
           parser->Convert<bool>(parser->GetOption('h')->GetFunction()->GetName()))
  {
    parser->PrintMenu(std::cout, 5, true);
    return EXIT_SUCCESS;
  }

  // Get dimensionality

  std::string filename;

  itk::ants::CommandLineParser::OptionType::Pointer imageOption = parser->GetOption("input-image");
  if (imageOption && imageOption->GetNumberOfFunctions() > 0)
  {
    filename = imageOption->GetFunction(0)->GetName();

    itk::ImageIOBase::Pointer imageIO =
      itk::ImageIOFactory::CreateImageIO(filename.c_str(), itk::IOFileModeEnum::ReadMode);
    unsigned int dimension = imageIO->GetNumberOfDimensions();

    if (dimension == 3)
    {
      return CreateMosaic(parser);
    }
    else
    {
      std::cout << "Unsupported dimension" << std::endl;
      return EXIT_FAILURE;
    }
  }
  else
  {
    std::cout << "Input image not specified." << std::endl;
    return EXIT_FAILURE;
  }


  return EXIT_SUCCESS;
}
} // namespace ants
