#include "antsUtilities.h"
#include "antsAllocImage.h"
#include "itkImageFileReader.h"
#include "itkVariableLengthVector.h"
#include "itkImageFileWriter.h"
#include "itkMatrixOffsetTransformBase.h"
#include "itkTransformFactory.h"
#include "itkTransformFileReader.h"
#include "itkVectorNearestNeighborInterpolateImageFunction.h"
#include "ReadWriteData.h"
#include "itkWarpImageMultiTransformFilter.h"
#include "itkExtractImageFilter.h"

namespace ants
{
static bool
WarpTimeSeriesImageMultiTransform_ParseInput(int              argc,
                                             char **          argv,
                                             char *&          moving_image_filename,
                                             char *&          output_image_filename,
                                             TRAN_OPT_QUEUE & opt_queue,
                                             MISC_OPT &       misc_opt)
{
  opt_queue.clear();
  opt_queue.reserve(argc - 2);

  misc_opt.reference_image_filename = nullptr;
  misc_opt.use_NN_interpolator = false;
  misc_opt.use_TightestBoundingBox = false;
  misc_opt.use_RotationHeader = false;

  moving_image_filename = argv[0];
  output_image_filename = argv[1];

  int  ind = 2;
  bool set_current_affine_inv = false;

  while (ind < argc)
  {
    if (strcmp(argv[ind], "--use-NN") == 0)
    {
      misc_opt.use_NN_interpolator = true;
    }
    else if (strcmp(argv[ind], "-R") == 0)
    {
      ind++;
      if (ind >= argc)
      {
        return false;
      }
      misc_opt.reference_image_filename = argv[ind];
    }
    else if ((strcmp(argv[ind], "--tightest-bounding-box") == 0) && (strcmp(argv[ind], "-R") != 0))
    {
      misc_opt.use_TightestBoundingBox = true;
    }
    else if (strcmp(argv[ind], "--reslice-by-header") == 0)
    {
      misc_opt.use_RotationHeader = true;
      TRAN_OPT opt;
      opt.file_type = IMAGE_AFFINE_HEADER;
      opt.do_affine_inv = false;
      opt_queue.push_back(opt);
    }
    else if (strcmp(argv[ind], "--Id") == 0)
    {
      TRAN_OPT opt;
      opt.filename = "--Id";
      opt.do_affine_inv = false;
      opt.file_type = IDENTITY_TRANSFORM;
      opt_queue.push_back(opt);
    }
    else if (strcmp(argv[ind], "--moving-image-header") == 0 || strcmp(argv[ind], "-mh") == 0)
    {
      TRAN_OPT opt;
      opt.file_type = IMAGE_AFFINE_HEADER;
      opt.filename = moving_image_filename;
      //            opt.do_affine_inv = false;
      SetAffineInvFlag(opt, set_current_affine_inv);
      opt_queue.push_back(opt);
    }
    else if (strcmp(argv[ind], "--reference-image-header") == 0 || strcmp(argv[ind], "-rh") == 0)
    {
      if (misc_opt.reference_image_filename == nullptr)
      {
        std::cout
          << "reference image filename is not given yet. Specify it with -R before --reference-image-header / -rh."
          << std::endl;
        return false;
      }

      TRAN_OPT opt;
      opt.file_type = IMAGE_AFFINE_HEADER;
      opt.filename = misc_opt.reference_image_filename;
      //            opt.do_affine_inv = false;
      SetAffineInvFlag(opt, set_current_affine_inv);
      opt_queue.push_back(opt);
    }
    else if (strcmp(argv[ind], "-i") == 0)
    {
      set_current_affine_inv = true;
    }

    else if (strcmp(argv[ind], "--ANTS-prefix") == 0)
    {
      ind++;
      std::string prefix = argv[ind];
      std::string path, name, ext;
      FilePartsWithgz(prefix, path, name, ext);
      if (ext.empty())
      {
        ext = ".nii.gz";
      }

      std::string deform_file_name, x_deform_name;
      deform_file_name = path + name + std::string("Warp") + ext;
      x_deform_name = path + name + std::string("Warpxvec") + ext;
      if (CheckFileExistence(x_deform_name.c_str()))
      {
        TRAN_OPT opt;
        opt.filename = deform_file_name.c_str();
        opt.file_type = CheckFileType(opt.filename.c_str());
        opt.do_affine_inv = false;
        opt_queue.push_back(opt);
        std::cout << "found deformation file: " << opt.filename << std::endl;
        DisplayOpt(opt);
      }

      std::string affine_file_name;
      affine_file_name = path + name + std::string("Affine.txt");
      if (CheckFileExistence(affine_file_name.c_str()))
      {
        TRAN_OPT opt;
        opt.filename = affine_file_name.c_str();
        opt.file_type = CheckFileType(opt.filename.c_str());
        opt.do_affine_inv = false;
        opt_queue.push_back(opt);
        std::cout << "found affine file: " << opt.filename << std::endl;
        DisplayOpt(opt);
      }
    }
    else if (strcmp(argv[ind], "--ANTS-prefix-invert") == 0)
    {
      ind++;
      std::string prefix = argv[ind];
      std::string path, name, ext;
      FilePartsWithgz(prefix, path, name, ext);
      if (ext.empty())
      {
        ext = ".nii.gz";
      }

      std::string affine_file_name;
      affine_file_name = path + name + std::string("Affine.txt");
      if (CheckFileExistence(affine_file_name.c_str()))
      {
        TRAN_OPT opt;
        opt.filename = affine_file_name.c_str();
        opt.file_type = CheckFileType(opt.filename.c_str());
        opt.do_affine_inv = true;
        opt_queue.push_back(opt);
        std::cout << "found affine file: " << opt.filename << std::endl;
        DisplayOpt(opt);
      }

      std::string deform_file_name, x_deform_name;
      deform_file_name = path + name + std::string("InverseWarp.nii.gz");
      x_deform_name = path + name + std::string("InverseWarpxvec.nii.gz");
      if (CheckFileExistence(x_deform_name.c_str()))
      {
        TRAN_OPT opt;
        opt.filename = deform_file_name.c_str();
        opt.file_type = CheckFileType(opt.filename.c_str());
        opt.do_affine_inv = false;
        opt_queue.push_back(opt);
        std::cout << "found deformation file: " << opt.filename << std::endl;
        DisplayOpt(opt);
      }
    }
    else
    {
      TRAN_OPT opt;
      opt.filename = argv[ind];
      opt.file_type = CheckFileType(opt.filename.c_str());
      opt.do_affine_inv = false;
      if (opt.file_type == AFFINE_FILE)
      {
        SetAffineInvFlag(opt, set_current_affine_inv);
      }
      else if (opt.file_type == DEFORMATION_FILE && set_current_affine_inv)
      {
        std::cout << "Ignore inversion of non-affine file type! " << std::endl;
        std::cout << "opt.do_affine_inv:" << opt.do_affine_inv << std::endl;
      }

      opt_queue.push_back(opt);
      DisplayOpt(opt);
    }
    ind++;
  }

  if (misc_opt.use_RotationHeader)
  {
    //                if (misc_opt.reference_image_filename) {
    //                    opt_queue[0].filename = misc_opt.reference_image_filename;
    //                } else {
    opt_queue[0].filename = "--Id";
    opt_queue[0].file_type = IDENTITY_TRANSFORM;
    opt_queue[0].do_affine_inv = false;
    //                }

    //               TRAN_OPT opt;
    //               opt.file_type = IMAGE_AFFINE_HEADER;
    //               opt.filename = moving_image_filename;
    //               opt.do_affine_inv = true;
    //               opt_queue.push_back(opt);
    //
    //               std::cout << "Use Rotation Header!" << std::endl;
  }

  return true;
}

template <typename AffineTransformPointer>
void
GetIdentityTransform(AffineTransformPointer & aff)
{
  using AffineTransform = typename AffineTransformPointer::ObjectType;
  aff = AffineTransform::New();
  aff->SetIdentity();
}

template <int ImageDimension>
void
WarpImageMultiTransformFourD(char *           moving_image_filename,
                             char *           output_image_filename,
                             TRAN_OPT_QUEUE & opt_queue,
                             MISC_OPT &       misc_opt)
{
  using VectorImageType = itk::Image<float, ImageDimension>;                // 4D contains functional image
  using ImageType = itk::Image<float, ImageDimension - 1>;                  // 3D image domain -R option
  using VectorType = itk::Vector<float, ImageDimension - 1>;                // 3D warp
  using DisplacementFieldType = itk::Image<VectorType, ImageDimension - 1>; // 3D Field
  using AffineTransformType = itk::MatrixOffsetTransformBase<double, ImageDimension - 1, ImageDimension - 1>;
  using WarperType =
    itk::WarpImageMultiTransformFilter<ImageType, ImageType, DisplacementFieldType, AffineTransformType>;

  itk::TransformFactory<AffineTransformType>::RegisterTransform();


  typename VectorImageType::Pointer img_mov;

  ReadImage<VectorImageType>(img_mov, moving_image_filename);
  std::cout << " Four-D image size: " << img_mov->GetLargestPossibleRegion().GetSize() << std::endl;
  typename ImageType::Pointer img_ref;
  if (misc_opt.reference_image_filename)
  {
    ReadImage<ImageType>(img_ref, misc_opt.reference_image_filename);
  }

  using ExtractFilterType = itk::ExtractImageFilter<VectorImageType, ImageType>;

  // ORIENTATION ALERT -- the way this code sets up
  // transformedvecimage doesn't really make complete sense to me. In
  // particular, the 'grab upper dim-1 x dim-1 of directions' method
  // of setting lower-dimension dir cosines can lead to singular mattrices.
  // allocate output image
  typename VectorImageType::RegionType region = img_mov->GetLargestPossibleRegion();
  for (unsigned int i = 0; i < ImageDimension - 1; i++)
  {
    region.SetSize(i, img_ref->GetLargestPossibleRegion().GetSize()[i]);
  }
  typename VectorImageType::Pointer transformedvecimage = AllocImage<VectorImageType>(region);

  typename VectorImageType::DirectionType direction = transformedvecimage->GetDirection();
  direction.Fill(0);
  typename VectorImageType::PointType   origin;
  typename VectorImageType::SpacingType spc;
  for (unsigned int i = 0; i < ImageDimension - 1; i++)
  {
    for (unsigned int j = 0; j < ImageDimension - 1; j++)
    {
      direction[i][j] = img_ref->GetDirection()[i][j];
    }
    spc[i] = img_ref->GetSpacing()[i];
    origin[i] = img_ref->GetOrigin()[i];
  }
  direction[ImageDimension - 1][ImageDimension - 1] = 1;
  origin[ImageDimension - 1] = img_mov->GetOrigin()[ImageDimension - 1];
  spc[ImageDimension - 1] = img_mov->GetSpacing()[ImageDimension - 1];
  transformedvecimage->SetDirection(direction);
  transformedvecimage->SetSpacing(spc);
  transformedvecimage->SetOrigin(origin);

  std::cout << " 4D-In-Spc " << img_mov->GetSpacing() << std::endl;
  std::cout << " 4D-In-Org " << img_mov->GetOrigin() << std::endl;
  std::cout << " 4D-In-Size " << img_mov->GetLargestPossibleRegion().GetSize() << std::endl;
  std::cout << " 4D-In-Dir " << img_mov->GetDirection() << std::endl;
  std::cout << " ...... " << std::endl;
  std::cout << " 4D-Out-Spc " << transformedvecimage->GetSpacing() << std::endl;
  std::cout << " 4D-Out-Org " << transformedvecimage->GetOrigin() << std::endl;
  std::cout << " 4D-Out-Size " << transformedvecimage->GetLargestPossibleRegion().GetSize() << std::endl;
  std::cout << " 4D-Out-Dir " << transformedvecimage->GetDirection() << std::endl;

  unsigned int timedims = img_mov->GetLargestPossibleRegion().GetSize()[ImageDimension - 1];
  for (unsigned int timedim = 0; timedim < timedims; timedim++)
  {
    typename WarperType::Pointer warper = WarperType::New();
    warper->SetEdgePaddingValue(0);

    if (misc_opt.use_NN_interpolator)
    {
      using NNInterpolateType =
        typename itk::NearestNeighborInterpolateImageFunction<ImageType, typename WarperType::CoordinateType>;
      typename NNInterpolateType::Pointer interpolator_NN = NNInterpolateType::New();
      std::cout << " Use Nearest Neighbor interpolation " << std::endl;
      warper->SetInterpolator(interpolator_NN);
    }

    using TranReaderType = itk::TransformFileReader;
    using FieldReaderType = itk::ImageFileReader<DisplacementFieldType>;

    unsigned int transcount = 0;
    const int    kOptQueueSize = opt_queue.size();
    for (int i = 0; i < kOptQueueSize; i++)
    {
      const TRAN_OPT & opt = opt_queue[i];

      switch (opt.file_type)
      {
        case AFFINE_FILE:
        {
          typename TranReaderType::Pointer tran_reader = TranReaderType::New();
          tran_reader->SetFileName(opt.filename);
          tran_reader->Update();
          typename AffineTransformType::Pointer aff =
            dynamic_cast<AffineTransformType *>((tran_reader->GetTransformList())->front().GetPointer());
          if (opt.do_affine_inv)
          {
            typename AffineTransformType::Pointer aff_inv = AffineTransformType::New();
            aff->GetInverse(aff_inv);
            aff = aff_inv;
          }
          // std::cout <<" aff " << transcount <<  std::endl;
          warper->PushBackAffineTransform(aff);
          if (transcount == 0)
          {
            warper->SetOutputParametersFromImage(img_ref);
          }
          transcount++;
        }
        break;
        case IDENTITY_TRANSFORM:
        {
          typename AffineTransformType::Pointer aff;
          GetIdentityTransform(aff);
          // std::cout << " aff id" << transcount << std::endl;
          warper->PushBackAffineTransform(aff);
          transcount++;
        }
        break;
        case DEFORMATION_FILE:
        {
          typename FieldReaderType::Pointer field_reader = FieldReaderType::New();
          field_reader->SetFileName(opt.filename);
          field_reader->Update();
          typename DisplacementFieldType::Pointer field = field_reader->GetOutput();

          warper->PushBackDisplacementFieldTransform(field);
          warper->SetOutputParametersFromImage(field);

          transcount++;
        }
        break;
        default:
        {
          std::cout << "Unknown file type!" << std::endl;
        }
      }
    }

    // warper->PrintTransformList();
    if (img_ref.IsNotNull())
    {
      warper->SetOutputParametersFromImage(img_ref);
    }
    else
    {
      if (misc_opt.use_TightestBoundingBox == true)
      {
        // compute the desired spacking after inputting all the transform files using the
        std::cout << " not implemented " << std::endl;
        /*
          typename ImageType::SizeType largest_size;
          typename ImageType::PointType origin_warped;
          GetLaregstSizeAfterWarp(warper, warpthisimage , largest_size, origin_warped);
          warper->SetOutputParametersFromImage( warpthisimage );
          warper->SetOutputSize(largest_size);
          warper->SetOutputOrigin(origin_warped);
          {
          typename ImageType::DirectionType d;
          d.SetIdentity();
          warper->SetOutputDirection(d);
          }
          */
      }
    }

    if (timedim % std::max(timedims / 10, static_cast<unsigned int>(1)) == 0)
    {
      std::cout << (float)timedim / (float)timedims * 100 << " % done ... " << std::flush;
    }
    typename VectorImageType::RegionType extractRegion = img_mov->GetLargestPossibleRegion();
    extractRegion.SetSize(ImageDimension - 1, 0);
    extractRegion.SetIndex(ImageDimension - 1, timedim);
    typename ExtractFilterType::Pointer extractFilter = ExtractFilterType::New();
    extractFilter->SetInput(img_mov);
    extractFilter->SetDirectionCollapseToSubmatrix();
    extractFilter->SetExtractionRegion(extractRegion);
    extractFilter->Update();
    typename ImageType::Pointer       warpthisimage = extractFilter->GetOutput();
    typename ImageType::SpacingType   qspc = warpthisimage->GetSpacing();
    typename ImageType::PointType     qorg = warpthisimage->GetOrigin();
    typename ImageType::DirectionType qdir = warpthisimage->GetDirection();
    qdir.Fill(0);
    for (unsigned int qq = 0; qq < ImageDimension - 1; qq++)
    {
      for (unsigned int pp = 0; pp < ImageDimension - 1; pp++)
      {
        qdir[qq][pp] = img_mov->GetDirection()[qq][pp];
      }
      qspc[qq] = img_mov->GetSpacing()[qq];
      qorg[qq] = img_mov->GetOrigin()[qq];
    }
    warpthisimage->SetSpacing(qspc);
    warpthisimage->SetOrigin(qorg);
    warpthisimage->SetDirection(qdir);

    warper->SetInput(warpthisimage);
    warper->DetermineFirstDeformNoInterp();
    warper->Update();

    using Iterator = itk::ImageRegionIteratorWithIndex<ImageType>;
    Iterator vfIter2(warper->GetOutput(), warper->GetOutput()->GetLargestPossibleRegion());
    for (vfIter2.GoToBegin(); !vfIter2.IsAtEnd(); ++vfIter2)
    {
      typename ImageType::PixelType       fval = vfIter2.Get();
      typename VectorImageType::IndexType ind;
      for (unsigned int xx = 0; xx < ImageDimension - 1; xx++)
      {
        ind[xx] = vfIter2.GetIndex()[xx];
      }
      ind[ImageDimension - 1] = timedim;
      transformedvecimage->SetPixel(ind, fval);
      //    if ( ind[0] == 53 && ind[1] == 19 && ind[2] == 30 ) std::cout << " fval " << fval << " td " << timedim <<
      // std::endl;
    }

    if (timedim == 0)
    {
      std::cout << warper->GetOutput()->GetDirection() << std::endl;
    }
  }
  std::cout << " 100 % complete " << std::endl;
  ANTs::WriteImage<VectorImageType>(transformedvecimage, output_image_filename);
}

template <int ImageDimension>
void
WarpImageMultiTransform(char *           moving_image_filename,
                        char *           output_image_filename,
                        TRAN_OPT_QUEUE & opt_queue,
                        MISC_OPT &       misc_opt)
{
  using VectorImageType = itk::VectorImage<float, ImageDimension>;
  using ImageType = itk::Image<float, ImageDimension>;
  using VectorType = itk::Vector<float, ImageDimension>;
  using DisplacementFieldType = itk::Image<VectorType, ImageDimension>;
  using AffineTransformType = itk::MatrixOffsetTransformBase<double, ImageDimension, ImageDimension>;
  using WarperType =
    itk::WarpImageMultiTransformFilter<ImageType, ImageType, DisplacementFieldType, AffineTransformType>;

  itk::TransformFactory<AffineTransformType>::RegisterTransform();

  typename VectorImageType::Pointer  img_mov;
  typename itk::ImageIOBase::Pointer imageIO =
    itk::ImageIOFactory::CreateImageIO(moving_image_filename, itk::IOFileModeEnum::ReadMode);
  imageIO->SetFileName(moving_image_filename);
  imageIO->ReadImageInformation();
  //    std::cout << " Dimension " << imageIO->GetNumberOfDimensions()  << " Components "
  // <<imageIO->GetNumberOfComponents() << std::endl;
  unsigned int veclength = imageIO->GetNumberOfComponents();
  std::cout << " read veclength as:: " << veclength << std::endl;
  ReadImage<VectorImageType>(img_mov, moving_image_filename);
  typename ImageType::Pointer img_ref;

  if (misc_opt.reference_image_filename)
  {
    ReadImage<ImageType>(img_ref, misc_opt.reference_image_filename);
  }

  typename VectorImageType::Pointer img_output = AllocImage<VectorImageType>(img_ref);
  img_output->SetNumberOfComponentsPerPixel(veclength);

  typename ImageType::IndexType index;
  index.Fill(0);
  typename VectorImageType::PixelType vec = img_mov->GetPixel(index);
  vec.Fill(0);
  img_output->FillBuffer(vec);
  for (unsigned int tensdim = 0; tensdim < veclength; tensdim++)
  {
    using IndexSelectCasterType = itk::VectorIndexSelectionCastImageFilter<VectorImageType, ImageType>;
    typename IndexSelectCasterType::Pointer fieldCaster = IndexSelectCasterType::New();
    fieldCaster->SetInput(img_mov);
    fieldCaster->SetIndex(tensdim);
    fieldCaster->Update();
    typename ImageType::Pointer tenscomponent = fieldCaster->GetOutput();
    tenscomponent->SetSpacing(img_mov->GetSpacing());
    tenscomponent->SetOrigin(img_mov->GetOrigin());
    tenscomponent->SetDirection(img_mov->GetDirection());

    typename WarperType::Pointer warper = WarperType::New();
    warper->SetInput(tenscomponent);
    //      PixelType nullPix;
    // nullPix.Fill(0);
    warper->SetEdgePaddingValue(0);

    if (misc_opt.use_NN_interpolator)
    {
      using NNInterpolateType =
        typename itk::NearestNeighborInterpolateImageFunction<ImageType, typename WarperType::CoordinateType>;
      typename NNInterpolateType::Pointer interpolator_NN = NNInterpolateType::New();
      std::cout << "Haha" << std::endl;
      warper->SetInterpolator(interpolator_NN);
    }

    using TranReaderType = itk::TransformFileReader;
    using FieldReaderType = itk::ImageFileReader<DisplacementFieldType>;

    unsigned int transcount = 0;
    const int    kOptQueueSize = opt_queue.size();
    for (int i = 0; i < kOptQueueSize; i++)
    {
      const TRAN_OPT & opt = opt_queue[i];

      switch (opt.file_type)
      {
        case AFFINE_FILE:
        {
          typename TranReaderType::Pointer tran_reader = TranReaderType::New();
          tran_reader->SetFileName(opt.filename);
          tran_reader->Update();
          typename AffineTransformType::Pointer aff =
            dynamic_cast<AffineTransformType *>((tran_reader->GetTransformList())->front().GetPointer());
          if (opt.do_affine_inv)
          {
            typename AffineTransformType::Pointer aff_inv = AffineTransformType::New();
            aff->GetInverse(aff_inv);
            aff = aff_inv;
          }
          // std::cout <<" aff " << transcount <<  std::endl;
          warper->PushBackAffineTransform(aff);
          if (transcount == 0)
          {
            warper->SetOutputParametersFromImage(img_mov);
          }
          transcount++;
        }
        break;
        case IDENTITY_TRANSFORM:
        {
          typename AffineTransformType::Pointer aff;
          GetIdentityTransform(aff);
          // std::cout << " aff id" << transcount << std::endl;
          warper->PushBackAffineTransform(aff);
          transcount++;
        }
        break;
        case DEFORMATION_FILE:
        {
          typename FieldReaderType::Pointer field_reader = FieldReaderType::New();
          field_reader->SetFileName(opt.filename);
          field_reader->Update();
          typename DisplacementFieldType::Pointer field = field_reader->GetOutput();

          warper->PushBackDisplacementFieldTransform(field);
          warper->SetOutputParametersFromImage(field);

          transcount++;
        }
        break;
        default:
        {
          std::cout << "Unknown file type!" << std::endl;
        }
      }
    }

    // warper->PrintTransformList();

    if (img_ref.IsNotNull())
    {
      warper->SetOutputParametersFromImage(img_ref);
    }
    else
    {
      if (misc_opt.use_TightestBoundingBox == true)
      {
        // compute the desired spacking after inputting all the transform files using the

        typename ImageType::SizeType  largest_size;
        typename ImageType::PointType origin_warped;
        GetLargestSizeAfterWarp<WarperType, VectorImageType>(warper, img_mov, largest_size, origin_warped);
        warper->SetOutputParametersFromImage(img_mov);
        warper->SetOutputSize(largest_size);
        warper->SetOutputOrigin(origin_warped);
        {
          typename ImageType::DirectionType d;
          d.SetIdentity();
          warper->SetOutputDirection(d);
        }
      }
    }

    warper->DetermineFirstDeformNoInterp();
    warper->Update();

    using Iterator = itk::ImageRegionIteratorWithIndex<VectorImageType>;
    Iterator vfIter2(img_output, img_output->GetLargestPossibleRegion());
    for (vfIter2.GoToBegin(); !vfIter2.IsAtEnd(); ++vfIter2)
    {
      typename VectorImageType::PixelType tens = vfIter2.Get();
      tens[tensdim] = warper->GetOutput()->GetPixel(vfIter2.GetIndex());
      vfIter2.Set(tens);
    }
  }
  ANTs::WriteImage<VectorImageType>(img_output, output_image_filename);
}

// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int
WarpTimeSeriesImageMultiTransform(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(), "WarpTimeSeriesImageMultiTransform");

  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 );

  if (argc <= 3)
  {
    std::cout << "\nUsage 1 (Forward warp): " << argv[0]
              << " ImageDimension <moving_image.ext> <output_image.ext> -R <fixed_image.ext> <MyWarp.ext> "
                 "<MyAffine.txt> [interpolation]"
              << std::endl;

    std::cout << "\nUsage 2 (Inverse warp): " << argv[0]
              << " ImageDimension <fixed_image.ext> <output_image.ext> -R <moving_image.ext> -i <MyAffine.txt> "
                 "<MyInverseWarp.ext> [interpolation]"
              << std::endl;

    std::cout << "\nUsage Information " << std::endl;
    std::cout << " ImageDimension            : 3 or 4 (required argument)." << std::endl;
    std::cout << " <moving_image.ext>        : The image to apply the transformation to. The moving_image will be "
                 "either a 3-D image with vector voxels or a 4D image with scalar voxels."
              << std::endl;
    std::cout << " <output_image.ext>        : The resulting image. Output will be of the same type as input, but will "
                 "be resampled to the domain size defined by the -R image."
              << std::endl;
    std::cout << " <MyWarp.ext> <MyAffine.txt>    : Mappings can be stringed together, e.g.: MyAffine.txt "
                 "MySecondAffine.txt MyWarp.nii.gz MySecondWarp.nii.gz -i MyInverseAffine.txt"
              << std::endl;

    std::cout << "\nOptions:" << std::endl;
    std::cout << " -i                : Will use the inversion of the following affine transform." << std::endl;
    std::cout << " \n -R                : Reference image space that you wish to warp into." << std::endl;
    std::cout << " --reslice-by-header        : Equivalient to -i -mh, or -fh -i -mh if used together with -R. It uses "
                 "the orientation matrix and origin encoded in the image file header. "
              << std::endl;
    std::cout << " --tightest-bounding-box    : Computes the tightest bounding box using all the affine "
                 "transformations. It will be overrided by -R <reference_image.ext> if given."
              << std::endl;
    std::cout
      << " These options can be used together with -R and are typically not used together with any other transforms."
      << std::endl;

    std::cout << "\nInterpolation:" << std::endl;
    std::cout << " --use-NN            : Use Nearest Neighbor Interpolator" << std::endl;
    std::cout << " --use-BSpline            : Use 3rd order B-Spline Interpolation." << std::endl;

    std::cout << "\n " << std::endl;
    if (argc >= 2 && (std::string(argv[1]) == std::string("--help") || std::string(argv[1]) == std::string("-h")))
    {
      return EXIT_SUCCESS;
    }
    return EXIT_FAILURE;
  }

  TRAN_OPT_QUEUE opt_queue;
  char *         moving_image_filename = nullptr;
  char *         output_image_filename = nullptr;

  MISC_OPT misc_opt;

  int kImageDim = std::stoi(argv[1]);

  const bool is_parsing_ok = WarpTimeSeriesImageMultiTransform_ParseInput(
    argc - 2, argv + 2, moving_image_filename, output_image_filename, opt_queue, misc_opt);

  if (is_parsing_ok)
  {
    std::cout << "moving_image_filename: " << moving_image_filename << std::endl;
    std::cout << "output_image_filename: " << output_image_filename << std::endl;
    std::cout << "reference_image_filename: ";
    if (misc_opt.reference_image_filename)
    {
      std::cout << misc_opt.reference_image_filename << std::endl;
    }
    else
    {
      std::cout << "NULL" << std::endl;
    }
    DisplayOptQueue(opt_queue);

    switch (kImageDim)
    {
      case 2:
      {
        WarpImageMultiTransform<2>(moving_image_filename, output_image_filename, opt_queue, misc_opt);
      }
      break;
      case 3:
      {
        WarpImageMultiTransform<3>(moving_image_filename, output_image_filename, opt_queue, misc_opt);
      }
      break;
      case 4:
      {
        WarpImageMultiTransformFourD<4>(moving_image_filename, output_image_filename, opt_queue, misc_opt);
      }
      break;
    }
  }
  else
  {
    std::cout << "Input error!" << std::endl;
    return EXIT_FAILURE;
  }
  return EXIT_SUCCESS;
}
} // namespace ants
