

#include "antsUtilities.h"
#include "antsAllocImage.h"
#include <algorithm>

#include "itkVectorIndexSelectionCastImageFilter.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "vnl/algo/vnl_determinant.h"
#include "itkANTSImageRegistrationOptimizer.h"
#include "itkTimeVaryingVelocityFieldIntegrationImageFilter.h"
#include "itkWarpImageFilter.h"
#include "itkTimeVaryingVelocityFieldTransform.h"

#include "itkImageFileWriter.h"

#include "itkRescaleIntensityImageFilter.h"
#include "vnl/algo/vnl_determinant.h"
#include "itkDiscreteGaussianImageFilter.h"
#include "itkVectorLinearInterpolateImageFunction.h"
#include "itkGradientRecursiveGaussianImageFilter.h"
#include "itkVectorCurvatureAnisotropicDiffusionImageFilter.h"
#include "itkLaplacianRecursiveGaussianImageFilter.h"
#include "itkGradientRecursiveGaussianImageFilter.h"

#include "ReadWriteData.h"

namespace ants
{
template <unsigned int ImageDimension>
int
IntegrateVelocityField(int argc, char * argv[])
{
  int         argct = 1;
  std::string imgfn = std::string(argv[argct]);
  argct++;

  std::string vectorfn = std::string(argv[argct]);
  argct++;
  std::string outname = std::string(argv[argct]);
  argct++;

  using PixelType = float;
  PixelType timezero = 0;
  PixelType timeone = 1;
  PixelType dT = 0.01;
  if (argc > argct)
  {
    timezero = atof(argv[argct]);
  }
  argct++;
  if (argc > argct)
  {
    timeone = atof(argv[argct]);
  }
  argct++;
  if (argc > argct)
  {
    dT = atof(argv[argct]);
  }
  argct++;
  std::cout << " time-0 " << timezero << " dt " << dT << " time-1 " << timeone << std::endl;
  PixelType starttime = timezero;
  PixelType finishtime = timeone;
  using PixelType = float;
  using VectorType = itk::Vector<PixelType, ImageDimension>;
  using DisplacementFieldType = itk::Image<VectorType, ImageDimension>;
  using TimeVaryingVelocityFieldType = itk::Image<VectorType, ImageDimension + 1>;
  using ImageType = itk::Image<PixelType, ImageDimension>;

  typename ImageType::Pointer image;
  ReadImage<ImageType>(image, imgfn.c_str());
  using tvt = TimeVaryingVelocityFieldType;
  typename tvt::Pointer timeVaryingVelocity;
  ReadImage<tvt>(timeVaryingVelocity, vectorfn.c_str());

  VectorType zero;
  zero.Fill(0);
  typename DisplacementFieldType::Pointer deformation = AllocImage<DisplacementFieldType>(image, zero);

  if (!timeVaryingVelocity)
  {
    std::cerr << " No TV Field " << std::endl;
    return EXIT_FAILURE;
  }

  if (starttime < 0)
  {
    starttime = 0;
  }
  if (starttime > 1)
  {
    starttime = 1;
  }
  if (finishtime < 0)
  {
    finishtime = 0;
  }
  if (finishtime > 1)
  {
    finishtime = 1;
  }

  using IntegratorType =
    itk::TimeVaryingVelocityFieldIntegrationImageFilter<TimeVaryingVelocityFieldType, DisplacementFieldType>;
  typename IntegratorType::Pointer integrator = IntegratorType::New();
  integrator->SetInput(timeVaryingVelocity);
  integrator->SetLowerTimeBound(starttime);
  integrator->SetUpperTimeBound(finishtime);
  integrator->SetNumberOfIntegrationSteps((unsigned int)1 / dT);
  integrator->Update();

  ANTs::WriteImage<DisplacementFieldType>(integrator->GetOutput(), outname.c_str());
  return 0;
}

// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int
ANTSIntegrateVelocityField(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(), "ANTSIntegrateVelocityField");
  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 < 4)
  {
    std::cerr << "Usage:   " << argv[0] << " reference_image  VelocityIn.mhd DeformationOut.nii.gz  time0 time1 dT  "
              << 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;
  }
  std::cout << " start " << std::endl;
  std::string               ifn = std::string(argv[1]);
  itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(ifn.c_str(), itk::IOFileModeEnum::ReadMode);
  imageIO->SetFileName(ifn.c_str());
  imageIO->ReadImageInformation();
  unsigned int dim = imageIO->GetNumberOfDimensions();
  std::cout << " dim " << dim << std::endl;

  switch (dim)
  {
    case 2:
    {
      IntegrateVelocityField<2>(argc, argv);
    }
    break;
    case 3:
    {
      IntegrateVelocityField<3>(argc, argv);
    }
    break;
    case 4:
    {
      IntegrateVelocityField<4>(argc, argv);
    }
    break;
    default:
      std::cerr << "Unsupported dimension" << std::endl;
      return EXIT_FAILURE;
  }

  return EXIT_SUCCESS;
}
} // namespace ants
