/** ANTS Landmarks used to initialize an affine transform ... */

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

#include "itkLandmarkBasedTransformInitializer.h"
#include "itkImage.h"
#include "itkImageIOBase.h"
#include "itkImageIOFactory.h"
#include <cmath>
#include <iostream>
#include "ReadWriteData.h"
#include "itkTransformFileWriter.h"

#include <vnl/vnl_matrix.h>

#include "vnl/algo/vnl_qr.h"
namespace ants
{
// //////////////////////////////////////////////////////////////////////
// Stripped from ANTS_affine_registration2.h
template <typename TransformType>
void
WriteAffineTransformFile(typename TransformType::Pointer & transform, const std::string & filename)
{
  itk::TransformFileWriter::Pointer transform_writer;

  transform_writer = itk::TransformFileWriter::New();
  transform_writer->SetFileName(filename);
  transform_writer->SetInput(transform);
#if ITK_VERSION_MAJOR >= 5
  transform_writer->SetUseCompression(true);
#endif

  try
  {
    transform_writer->Update();
  }
  catch (const itk::ExceptionObject & itkNotUsed(err))
  {
    std::cerr << "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!" << std::endl
              << "Exception in writing transform file: " << std::endl
              << filename << std::endl;
    return;
  }
}

// //////////////////////////////////////////////////////////////////////
// Stripped from ANTS_affine_registration2.h
template <typename RunningAffineTransformPointerType, typename AffineTransformPointerType>
inline void
PostConversionInAffine(RunningAffineTransformPointerType & transform_running, AffineTransformPointerType & transform)
{
  using RunningAffineTransformType = typename RunningAffineTransformPointerType::ObjectType;
  using AffineTransformType = typename AffineTransformPointerType::ObjectType;

  transform->SetCenter(*(reinterpret_cast<typename AffineTransformType::InputPointType *>(
    const_cast<typename RunningAffineTransformType::InputPointType *>(&(transform_running->GetCenter())))));
  transform->SetTranslation(*(reinterpret_cast<typename AffineTransformType::OutputVectorType *>(
    const_cast<typename RunningAffineTransformType::OutputVectorType *>(&(transform_running->GetTranslation())))));
  transform->SetMatrix(*(reinterpret_cast<typename AffineTransformType::MatrixType *>(
    const_cast<typename RunningAffineTransformType::MatrixType *>(&(transform_running->GetMatrix())))));

  // std::cout << "transform_running" << transform_running << std::endl;
  // std::cout << "transform" << transform << std::endl;
}

template <typename TransformA, unsigned int ImageDimension>
void
DumpTransformForANTS3D(typename TransformA::Pointer & transform, const std::string & ANTS_prefix)
{
  // ANTS transform file type
  using AffineTransformType = itk::AffineTransform<double, ImageDimension>;
  typename AffineTransformType::Pointer transform_ANTS = AffineTransformType::New();
  std::string                           ANTS_affine_filename = ANTS_prefix;
  PostConversionInAffine(transform, transform_ANTS);
  WriteAffineTransformFile<AffineTransformType>(transform_ANTS, ANTS_affine_filename);
}

// ////////
// x: fixedLandmarks
// y: movingLandmarks
// (A,t,c) : affine transform, A:3*3, t: 3*1 c: 3*1 (c is the center of all points in x)
// y-c = A*(x-c) + t;
// steps:
// 1. c = average of points of x
// 2. let y1 = y-c; x1 = x - c; x11 = [x1; 1 ... 1] // extend x11
// 3. minimize (y1-A1*x11)^2, A1 is a 3*4 matrix
// 4. A = A1(1:3, 1:3), t = A1(1:3, 4);
// step 3:
//   A11 = (y1*x11')*(x11*x11')^(-1)
// type info:
//   assume PointContainerType is std::vector
//   assume TrnasformPointerType is MatrixOffsetTransformBase

template <typename PointContainerType, typename TransformType, unsigned int Dim>
void
GetAffineTransformFromTwoPointSets(PointContainerType &              fixedLandmarks,
                                   PointContainerType &              movingLandmarks,
                                   typename TransformType::Pointer & transform)
{
  int n = fixedLandmarks.size();

  vnl_matrix<double> y(Dim, n), x(Dim, n);
  for (int i = 0; i < n; i++)
  {
    for (unsigned int j = 0; j < Dim; j++)
    {
      x(j, i) = fixedLandmarks[i][j];
      y(j, i) = movingLandmarks[i][j];
    }
  }

  vnl_vector<double> c(Dim);
  for (unsigned int j = 0; j < Dim; j++)
  {
    c[j] = x.get_row(j).mean();
  }

  vnl_matrix<double> y1(Dim, n), x11(Dim + 1, n);
  for (int i = 0; i < n; i++)
  {
    y1.set_column(i, y.get_column(i) - c);

    vnl_vector<double> x_tmp(Dim), x1_tmp(Dim + 1);
    x_tmp = x.get_column(i) - c;
    for (unsigned int j = 0; j < Dim; j++)
    {
      x1_tmp[j] = x_tmp[j];
    }
    x1_tmp[Dim] = 1;

    x11.set_column(i, x1_tmp);
  }

  vnl_matrix<double> A11(Dim, Dim + 1);
  vnl_matrix<double> x11t = x11.transpose();

  vnl_svd<double> qr(x11t); // can use vnl_qr
  A11 = qr.inverse() * (y1.transpose());
  A11 = A11.transpose();

  vnl_matrix<double> A(Dim, Dim);
  A = A11.extract(Dim, Dim, 0, 0);

  std::cout << "y=" << y << std::endl;
  std::cout << "x=" << x << std::endl;

  std::cout << "y1=" << y1 << std::endl;
  std::cout << "x11=" << x11 << std::endl;
  std::cout << "A11=" << A11 << std::endl;

  vnl_vector<double> t = A11.get_column(Dim);

  using PointType = typename TransformType::InputPointType;
  using VectorType = typename TransformType::OutputVectorType;
  using MatrixType = typename TransformType::MatrixType;

  PointType center;
  for (unsigned int i = 0; i < Dim; i++)
  {
    center[i] = c[i];
  }

  VectorType translation;
  for (unsigned int i = 0; i < Dim; i++)
  {
    translation[i] = t[i];
  }

  MatrixType matrix(A);

  transform->SetCenter(center);
  transform->SetTranslation(translation);
  transform->SetMatrix(matrix);
}

//
// The test specifies a bunch of fixed and moving landmarks and test if the
// fixed landmarks after transform by the computed transform coincides
// with the moving landmarks....

template <unsigned int Dimension>
int
LandmarkBasedTransformInitializerBA(int, char * argv[])
{
  using PixelType = float;
  using FixedImageType = itk::Image<PixelType, Dimension>;
  using MovingImageType = itk::Image<PixelType, Dimension>;
  using ImageType = itk::Image<PixelType, Dimension>;
  using Iterator = itk::ImageRegionIteratorWithIndex<ImageType>;
  typename ImageType::Pointer fixedimage;
  typename ImageType::Pointer movingimage;
  ReadImage<ImageType>(fixedimage, argv[1]);
  ReadImage<ImageType>(movingimage, argv[2]);

  bool bRigid = (strcmp(argv[3], "rigid") == 0);

  /** get all of the relevant labels in the fixed image and moving image */
  using LabelSetType = std::vector<PixelType>;
  LabelSetType myFixLabelSet;
  LabelSetType myMovLabelSet;
  /** count the labels in the image */
  Iterator It(fixedimage, fixedimage->GetLargestPossibleRegion());
  for (It.GoToBegin(); !It.IsAtEnd(); ++It)
  {
    PixelType label = It.Get();
    if (fabs(label) > 0)
    {
      if (find(myFixLabelSet.begin(), myFixLabelSet.end(), label) == myFixLabelSet.end())
      {
        //          std::cout <<" f-label " << label << std::endl;
        myFixLabelSet.push_back(label);
      }
    }
  }
  Iterator ItM(movingimage, movingimage->GetLargestPossibleRegion());
  for (ItM.GoToBegin(); !ItM.IsAtEnd(); ++ItM)
  {
    PixelType label = ItM.Get();
    if (fabs(label) > 0)
    {
      if (find(myMovLabelSet.begin(), myMovLabelSet.end(), label) == myMovLabelSet.end())
      {
        //          std::cout <<" m-label " << label << std::endl;
        myMovLabelSet.push_back(label);
      }
    }
  }

  std::sort(myFixLabelSet.begin(), myFixLabelSet.end());
  std::sort(myMovLabelSet.begin(), myMovLabelSet.end());

  LabelSetType::const_iterator fit;
  LabelSetType::const_iterator mit = myMovLabelSet.begin();
  for (fit = myFixLabelSet.begin(); fit != myFixLabelSet.end(); ++fit)
  {
    float fixlabel = *fit;
    float movlabel = *mit;
    std::cout << " fix-label " << fixlabel << " movlabel " << movlabel << std::endl;
    if (!itk::Math::FloatAlmostEqual(movlabel, fixlabel))
    {
      std::cout << " labels do not match -- exiting " << std::endl;
      exit(1);
    }
    ++mit;
  }

  // Set the transform type..
  using TransformType = itk::AffineTransform<double, Dimension>;
  typename TransformType::Pointer transform = TransformType::New();
  using TransformInitializerType =
    itk::LandmarkBasedTransformInitializer<TransformType, FixedImageType, MovingImageType>;
  typename TransformInitializerType::Pointer initializer = TransformInitializerType::New();

  // Set fixed and moving landmarks
  using PointsContainerType = typename TransformInitializerType::LandmarkPointContainer;
  PointsContainerType fixedLandmarks;
  PointsContainerType movingLandmarks;

  // compute the CoM's of all the landmarks
  typename ImageType::SpacingType spacing = fixedimage->GetSpacing();
  for (fit = myFixLabelSet.begin(); fit != myFixLabelSet.end(); ++fit)
  {
    float                                                currentlabel = *fit;
    float                                                totalct = 0;
    typename TransformInitializerType::LandmarkPointType myCenterOfMass;
    myCenterOfMass.Fill(0);
    for (It.GoToBegin(); !It.IsAtEnd(); ++It)
    {
      PixelType label = It.Get();
      if (fabs(label - currentlabel) < 0.001)
      {
        totalct++;
        // compute center of mass
        typename ImageType::PointType point;
        fixedimage->TransformIndexToPhysicalPoint(It.GetIndex(), point);
        for (unsigned int i = 0; i < spacing.Size(); i++)
        {
          myCenterOfMass[i] += point[i];
        }
        std::cout << " point " << point << std::endl;
      }
    }
    for (unsigned int i = 0; i < spacing.Size(); i++)
    {
      myCenterOfMass[i] /= static_cast<double>(totalct);
    }
    // std::cout << " pushing-fix " <<  myCenterOfMass << std::endl;
    fixedLandmarks.push_back(myCenterOfMass);
  }

  // compute the CoM's of all the landmarks
  spacing = movingimage->GetSpacing();
  for (mit = myMovLabelSet.begin(); mit != myMovLabelSet.end(); ++mit)
  {
    float currentlabel = *mit;
    float totalct = 0;
    using LandmarkPointType = typename TransformInitializerType::LandmarkPointType;
    LandmarkPointType myCenterOfMass;
    myCenterOfMass.Fill(0);
    for (ItM.GoToBegin(); !ItM.IsAtEnd(); ++ItM)
    {
      PixelType label = ItM.Get();
      if (itk::Math::FloatAlmostEqual(label, currentlabel))
      {
        totalct++;
        // compute center of mass
        typename ImageType::PointType point;
        movingimage->TransformIndexToPhysicalPoint(ItM.GetIndex(), point);
        for (unsigned int i = 0; i < spacing.Size(); i++)
        {
          myCenterOfMass[i] += point[i];
        }
      }
    }
    for (unsigned int i = 0; i < spacing.Size(); i++)
    {
      myCenterOfMass[i] /= static_cast<typename LandmarkPointType::CoordinateType>(totalct);
    }
    //    std::cout << " pushing-mov " <<  myCenterOfMass << std::endl;
    movingLandmarks.push_back(myCenterOfMass);
  }

  typename TransformInitializerType::PointsContainerConstIterator fitr = fixedLandmarks.begin();
  typename TransformInitializerType::PointsContainerConstIterator mitr = movingLandmarks.begin();
  while (mitr != movingLandmarks.end())
  {
    std::cout << "  Fixed Landmark: " << *fitr << " Moving landmark " << *mitr << std::endl;
    ++fitr;
    ++mitr;
  }

  initializer->SetFixedLandmarks(fixedLandmarks);
  initializer->SetMovingLandmarks(movingLandmarks);

  //  initializer->SetFixedImage( fixedimage );
  //  initializer->SetMovingImage( movingimage );
  initializer->SetTransform(transform);
  initializer->InitializeTransform();

  transform->Print(std::cout);
  // to transform a point
  //         transform->TransformPoint( *fitr ) << std::endl;

  // transform the transform to ANTS format
  std::string ANTS_prefix(argv[4]);

  using AffineTransformType = itk::AffineTransform<double, Dimension>;
  typename AffineTransformType::Pointer aff = AffineTransformType::New();

  GetAffineTransformFromTwoPointSets<PointsContainerType, AffineTransformType, Dimension>(
    fixedLandmarks, movingLandmarks, aff);

  std::cout << "affine:" << aff;

  if (bRigid)
  {
    DumpTransformForANTS3D<TransformType, Dimension>(transform, ANTS_prefix);
  }
  else
  {
    DumpTransformForANTS3D<AffineTransformType, Dimension>(aff, ANTS_prefix);
  }
  return EXIT_SUCCESS;
}

int
ANTSUseLandmarkImagesToGetAffineTransform(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(), "ANTSUseLandmarkImagesToGetAffineTransform");
  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 << "Usage:   " << argv[0]
              << " FixedImageWithLabeledLandmarks.nii.gz  MovingImageWithLabeledLandmarks.nii.gz [rigid | affine] "
                 "OutAffine.txt "
              << std::endl;
    std::cout
      << " we expect the input images to be (1) N-ary  (2) in the same physical space as the images you want to "
      << std::endl;
    std::cout << " register and (3 ) to have the same landmark points defined within them ... " << std::endl;
    std::cout << " landmarks will be defined from the center of mass of the labels in the input images . " << std::endl;
    std::cout << " You can use ITK-snap to generate the label images. " << 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;
  }

  // Get the image dimension
  std::string               fn = std::string(argv[1]);
  itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::IOFileModeEnum::ReadMode);
  imageIO->SetFileName(fn.c_str());
  imageIO->ReadImageInformation();

  switch (imageIO->GetNumberOfDimensions())
  {
    case 2:
    {
      LandmarkBasedTransformInitializerBA<2>(argc, argv);
    }
    break;
    case 3:
    {
      LandmarkBasedTransformInitializerBA<3>(argc, argv);
    }
    break;
    default:
      std::cerr << "Unsupported dimension" << std::endl;
      exit(EXIT_FAILURE);
  }
  return EXIT_SUCCESS;
}
} // namespace ants
