/*=========================================================================
 *
 *  Copyright UMC Utrecht and contributors
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *        http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef elxAdvancedBSplineTransform_hxx
#define elxAdvancedBSplineTransform_hxx

#include "elxAdvancedBSplineTransform.h"

#include "itkImageRegionExclusionConstIteratorWithIndex.h"
#include <vnl/vnl_math.h>


namespace elastix
{

/**
 * ************ InitializeBSplineTransform ***************
 */

template <typename TElastix>
unsigned int
AdvancedBSplineTransform<TElastix>::InitializeBSplineTransform()
{
  /** Initialize the right BSplineTransform and GridScheduleComputer. */
  if (this->m_Cyclic)
  {
    this->m_GridScheduleComputer = CyclicGridScheduleComputerType::New();
    this->m_GridScheduleComputer->SetBSplineOrder(this->m_SplineOrder);
    m_BSplineTransform =
      BSplineTransformBaseType::template Create<itk::CyclicBSplineDeformableTransform>(m_SplineOrder);
  }
  else
  {
    this->m_GridScheduleComputer = GridScheduleComputerType::New();
    this->m_GridScheduleComputer->SetBSplineOrder(this->m_SplineOrder);
    m_BSplineTransform =
      BSplineTransformBaseType::template Create<itk::AdvancedBSplineDeformableTransform>(m_SplineOrder);
  }

  this->SetCurrentTransform(this->m_BSplineTransform);
  this->m_GridUpsampler = GridUpsamplerType::New();
  this->m_GridUpsampler->SetBSplineOrder(this->m_SplineOrder);

  return 0;
} // end InitializeBSplineTransform()


/**
 * ******************* BeforeAll ***********************
 */

template <typename TElastix>
int
AdvancedBSplineTransform<TElastix>::BeforeAll()
{
  /** Read spline order and periodicity setting from configuration file. */
  this->m_SplineOrder = 3;
  this->GetConfiguration()->ReadParameter(
    this->m_SplineOrder, "BSplineTransformSplineOrder", this->GetComponentLabel(), 0, 0, true);
  this->m_Cyclic = false;
  this->GetConfiguration()->ReadParameter(this->m_Cyclic, "UseCyclicTransform", this->GetComponentLabel(), 0, 0, true);

  return this->InitializeBSplineTransform();
} // end BeforeAll()


/**
 * ******************* BeforeRegistration ***********************
 */

template <typename TElastix>
void
AdvancedBSplineTransform<TElastix>::BeforeRegistration()
{
  /** Set initial transform parameters to a 1x1x1 grid, with deformation (0,0,0).
   * In the method BeforeEachResolution() this will be replaced by the right grid size.
   * This seems not logical, but it is required, since the registration
   * class checks if the number of parameters in the transform is equal to
   * the number of parameters in the registration class. This check is done
   * before calling the BeforeEachResolution() methods.
   */

  /** Task 1 - Set the Grid. */

  /** Set gridsize for large dimension to 4 to prevent errors when checking
   * on support region size.
   */
  SizeType gridsize = SizeType::Filled(1);
  gridsize.SetElement(gridsize.GetSizeDimension() - 1, 4);

  /** Set it all. */
  this->m_BSplineTransform->SetGridRegion(RegionType(gridsize));
  this->m_BSplineTransform->SetGridSpacing(SpacingType(1.0));
  this->m_BSplineTransform->SetGridOrigin(OriginType());

  /** Task 2 - Give the registration an initial parameter-array. */
  this->m_Registration->GetAsITKBaseType()->SetInitialTransformParameters(
    ParametersType(this->GetNumberOfParameters(), 0.0));

  /** Precompute the B-spline grid regions. */
  this->PreComputeGridInformation();

} // end BeforeRegistration()


/**
 * ***************** BeforeEachResolution ***********************
 */

template <typename TElastix>
void
AdvancedBSplineTransform<TElastix>::BeforeEachResolution()
{
  /** What is the current resolution level? */
  unsigned int level = this->m_Registration->GetAsITKBaseType()->GetCurrentLevel();

  /** Define the grid. */
  if (level == 0)
  {
    this->InitializeTransform();
  }
  else
  {
    /** Upsample the B-spline grid, if required. */
    this->IncreaseScale();
  }

  /** Get the PassiveEdgeWidth and use it to set the OptimizerScales. */
  unsigned int passiveEdgeWidth = 0;
  this->GetConfiguration()->ReadParameter(
    passiveEdgeWidth, "PassiveEdgeWidth", this->GetComponentLabel(), level, 0, false);
  this->SetOptimizerScales(passiveEdgeWidth);

} // end BeforeEachResolution()


/**
 * ******************** PreComputeGridInformation ***********************
 */

template <typename TElastix>
void
AdvancedBSplineTransform<TElastix>::PreComputeGridInformation()
{
  /** Get the total number of resolution levels. */
  unsigned int nrOfResolutions = this->m_Registration->GetAsITKBaseType()->GetNumberOfLevels();

  /** Set up grid schedule computer with image info. */
  this->m_GridScheduleComputer->SetImageOrigin(this->GetElastix()->GetFixedImage()->GetOrigin());
  this->m_GridScheduleComputer->SetImageSpacing(this->GetElastix()->GetFixedImage()->GetSpacing());
  this->m_GridScheduleComputer->SetImageDirection(this->GetElastix()->GetFixedImage()->GetDirection());
  this->m_GridScheduleComputer->SetImageRegion(this->GetElastix()->GetFixedImage()->GetLargestPossibleRegion());

  /** Take the initial transform only into account, if composition is used. */
  if (this->GetUseComposition())
  {
    this->m_GridScheduleComputer->SetInitialTransform(this->Superclass1::GetInitialTransform());
  }

  /** Get the grid spacing schedule from the parameter file.
   *
   * Method 1: The user specifies "FinalGridSpacingInVoxels"
   * Method 2: The user specifies "FinalGridSpacingInPhysicalUnits"
   *
   * Method 1 and 2 additionally take the "GridSpacingSchedule".
   * The GridSpacingSchedule is defined by downsampling factors
   * for each resolution, for each dimension (just like the image
   * pyramid schedules). So, for 2D images, and 3 resulutions,
   * we can specify:
   * (GridSpacingSchedule 4.0 4.0 2.0 2.0 1.0 1.0)
   * Which is the default schedule, if no GridSpacingSchedule is supplied.
   */

  /** Determine which method is used. */
  bool        method1 = false;
  std::size_t count1 = this->m_Configuration->CountNumberOfParameterEntries("FinalGridSpacingInVoxels");
  if (count1 > 0)
  {
    method1 = true;
  }

  bool        method2 = false;
  std::size_t count2 = this->m_Configuration->CountNumberOfParameterEntries("FinalGridSpacingInPhysicalUnits");
  if (count2 > 0)
  {
    method2 = true;
  }

  /** Throw an exception if both methods are used. */
  if (count1 > 0 && count2 > 0)
  {
    itkExceptionMacro("ERROR: You can not specify both \"FinalGridSpacingInVoxels\""
                      " and \"FinalGridSpacingInPhysicalUnits\" in the parameter file.");
  }

  /** Declare variables and set defaults. */
  SpacingType finalGridSpacingInVoxels;
  SpacingType finalGridSpacingInPhysicalUnits;
  finalGridSpacingInVoxels.Fill(16.0);
  finalGridSpacingInPhysicalUnits.Fill(8.0);

  /** Method 1: Read the FinalGridSpacingInVoxels. */
  if (method1)
  {
    for (unsigned int dim = 0; dim < SpaceDimension; ++dim)
    {
      this->m_Configuration->ReadParameter(
        finalGridSpacingInVoxels[dim], "FinalGridSpacingInVoxels", this->GetComponentLabel(), dim, 0);
    }

    /** Compute the grid spacing in physical units. */
    for (unsigned int dim = 0; dim < SpaceDimension; ++dim)
    {
      finalGridSpacingInPhysicalUnits[dim] =
        finalGridSpacingInVoxels[dim] * this->GetElastix()->GetFixedImage()->GetSpacing()[dim];
    }
  }

  /** Method 2: Read the FinalGridSpacingInPhysicalUnits. */
  if (method2)
  {
    for (unsigned int dim = 0; dim < SpaceDimension; ++dim)
    {
      this->m_Configuration->ReadParameter(
        finalGridSpacingInPhysicalUnits[dim], "FinalGridSpacingInPhysicalUnits", this->GetComponentLabel(), dim, 0);
    }
  }

  /** Set up a default grid spacing schedule. */
  this->m_GridScheduleComputer->SetDefaultSchedule(nrOfResolutions);
  GridScheduleType gridSchedule = this->m_GridScheduleComputer->GetSchedule();

  /** Read what the user has specified. This overrules everything. */
  count2 = this->m_Configuration->CountNumberOfParameterEntries("GridSpacingSchedule");
  unsigned int entry_nr = 0;
  if (count2 == 0)
  {
    // keep the default schedule
  }
  else if (count2 == nrOfResolutions)
  {
    for (unsigned int res = 0; res < nrOfResolutions; ++res)
    {
      for (unsigned int dim = 0; dim < SpaceDimension; ++dim)
      {
        this->m_Configuration->ReadParameter(gridSchedule[res][dim], "GridSpacingSchedule", entry_nr, false);
      }
      ++entry_nr;
    }
  }
  else if (count2 == nrOfResolutions * SpaceDimension)
  {
    for (unsigned int res = 0; res < nrOfResolutions; ++res)
    {
      for (unsigned int dim = 0; dim < SpaceDimension; ++dim)
      {
        this->m_Configuration->ReadParameter(gridSchedule[res][dim], "GridSpacingSchedule", entry_nr, false);
        ++entry_nr;
      }
    }
  }
  else
  {
    log::error(std::ostringstream{}
               << "ERROR: Invalid GridSpacingSchedule! The number of entries behind the GridSpacingSchedule "
                  "option should equal the numberOfResolutions, or the numberOfResolutions * ImageDimension.");
    itkExceptionMacro("ERROR: Invalid GridSpacingSchedule!");
  }

  /** Output a warning that the gridspacing may be adapted to fit the Cyclic
   * behavior of the transform.
   */
  if (this->m_Cyclic)
  {
    log::warn(
      "WARNING: The provided grid spacing may be adapted to fit the cyclic behavior of the CyclicBSplineTransform.");
  }

  /** Set the grid schedule and final grid spacing in the schedule computer. */
  this->m_GridScheduleComputer->SetFinalGridSpacing(finalGridSpacingInPhysicalUnits);
  this->m_GridScheduleComputer->SetSchedule(gridSchedule);

  /** Compute the necessary information. */
  this->m_GridScheduleComputer->ComputeBSplineGrid();

} // end PreComputeGridInformation()


/**
 * ******************** InitializeTransform ***********************
 */

template <typename TElastix>
void
AdvancedBSplineTransform<TElastix>::InitializeTransform()
{
  /** Compute the B-spline grid region, origin, and spacing. */
  RegionType    gridRegion;
  OriginType    gridOrigin;
  SpacingType   gridSpacing;
  DirectionType gridDirection;
  this->m_GridScheduleComputer->GetBSplineGrid(0, gridRegion, gridSpacing, gridOrigin, gridDirection);

  /** Set it in the BSplineTransform. */
  this->m_BSplineTransform->SetGridRegion(gridRegion);
  this->m_BSplineTransform->SetGridSpacing(gridSpacing);
  this->m_BSplineTransform->SetGridOrigin(gridOrigin);
  this->m_BSplineTransform->SetGridDirection(gridDirection);

  /** Set initial parameters for the first resolution to 0.0. */
  ParametersType initialParameters(this->GetNumberOfParameters(), 0.0);
  this->m_Registration->GetAsITKBaseType()->SetInitialTransformParametersOfNextLevel(initialParameters);

} // end InitializeTransform()


/**
 * *********************** IncreaseScale ************************
 */

template <typename TElastix>
void
AdvancedBSplineTransform<TElastix>::IncreaseScale()
{
  /** What is the current resolution level? */
  unsigned int level = this->m_Registration->GetAsITKBaseType()->GetCurrentLevel();

  /** The current grid. */
  OriginType    currentGridOrigin = this->m_BSplineTransform->GetGridOrigin();
  SpacingType   currentGridSpacing = this->m_BSplineTransform->GetGridSpacing();
  RegionType    currentGridRegion = this->m_BSplineTransform->GetGridRegion();
  DirectionType currentGridDirection = this->m_BSplineTransform->GetGridDirection();

  /** The new required grid. */
  OriginType    requiredGridOrigin{};
  auto          requiredGridSpacing = itk::MakeFilled<SpacingType>(1.0);
  RegionType    requiredGridRegion;
  DirectionType requiredGridDirection;
  this->m_GridScheduleComputer->GetBSplineGrid(
    level, requiredGridRegion, requiredGridSpacing, requiredGridOrigin, requiredGridDirection);

  /** Get the latest transform parameters. */
  ParametersType latestParameters = this->m_Registration->GetAsITKBaseType()->GetLastTransformParameters();

  /** Setup the GridUpsampler. */
  this->m_GridUpsampler->SetCurrentGridOrigin(currentGridOrigin);
  this->m_GridUpsampler->SetCurrentGridSpacing(currentGridSpacing);
  this->m_GridUpsampler->SetCurrentGridRegion(currentGridRegion);
  this->m_GridUpsampler->SetCurrentGridDirection(currentGridDirection);
  this->m_GridUpsampler->SetRequiredGridOrigin(requiredGridOrigin);
  this->m_GridUpsampler->SetRequiredGridSpacing(requiredGridSpacing);
  this->m_GridUpsampler->SetRequiredGridRegion(requiredGridRegion);
  this->m_GridUpsampler->SetRequiredGridDirection(requiredGridDirection);

  /** Compute the upsampled B-spline parameters. */
  ParametersType upsampledParameters;
  this->m_GridUpsampler->UpsampleParameters(latestParameters, upsampledParameters);

  /** Set the new grid definition in the BSplineTransform. */
  this->m_BSplineTransform->SetGridOrigin(requiredGridOrigin);
  this->m_BSplineTransform->SetGridSpacing(requiredGridSpacing);
  this->m_BSplineTransform->SetGridRegion(requiredGridRegion);
  this->m_BSplineTransform->SetGridDirection(requiredGridDirection);

  /** Set the initial parameters for the next level. */
  this->m_Registration->GetAsITKBaseType()->SetInitialTransformParametersOfNextLevel(upsampledParameters);

  /** Set the parameters in the BsplineTransform. */
  this->m_BSplineTransform->SetParameters(
    this->m_Registration->GetAsITKBaseType()->GetInitialTransformParametersOfNextLevel());

} // end IncreaseScale()


/**
 * ************************* ReadFromFile ************************
 */

template <typename TElastix>
void
AdvancedBSplineTransform<TElastix>::ReadFromFile()
{
  /** Read spline order and periodicity settings and initialize BSplineTransform. */
  this->m_SplineOrder = 3;
  this->GetConfiguration()->ReadParameter(
    this->m_SplineOrder, "BSplineTransformSplineOrder", this->GetComponentLabel(), 0, 0);
  this->m_Cyclic = false;
  this->GetConfiguration()->ReadParameter(this->m_Cyclic, "UseCyclicTransform", this->GetComponentLabel(), 0, 0);
  this->InitializeBSplineTransform();

  /** Read and Set the Grid: this is a BSplineTransform specific task. */

  /** Declarations. Everything filled with default values.*/
  SizeType      gridsize = SizeType::Filled(1);
  IndexType     gridindex = { { 0 } };
  SpacingType   gridspacing(1.0);
  OriginType    gridorigin{};
  DirectionType griddirection = DirectionType::GetIdentity();

  /** Get GridSize, GridIndex, GridSpacing and GridOrigin. */
  for (unsigned int i = 0; i < SpaceDimension; ++i)
  {
    this->m_Configuration->ReadParameter(gridsize[i], "GridSize", i);
    this->m_Configuration->ReadParameter(gridindex[i], "GridIndex", i);
    this->m_Configuration->ReadParameter(gridspacing[i], "GridSpacing", i);
    this->m_Configuration->ReadParameter(gridorigin[i], "GridOrigin", i);

    // Retrieve grid direction cosines. (The matrix elements must be specified in column-major order.)
    for (unsigned int j = 0; j < SpaceDimension; ++j)
    {
      this->m_Configuration->ReadParameter(griddirection(j, i), "GridDirection", i * SpaceDimension + j);
    }
  }

  /** Set it all. */
  this->m_BSplineTransform->SetGridRegion(RegionType(gridindex, gridsize));
  this->m_BSplineTransform->SetGridSpacing(gridspacing);
  this->m_BSplineTransform->SetGridOrigin(gridorigin);
  this->m_BSplineTransform->SetGridDirection(griddirection);

  /** Call the ReadFromFile from the TransformBase.
   * This must be done after setting the Grid, because later the
   * ReadFromFile from TransformBase calls SetParameters, which
   * checks the parameter-size, which is based on the GridSize.
   */
  this->Superclass2::ReadFromFile();

} // end ReadFromFile()


/**
 * ************************* CreateDerivedTransformParameterMap ************************
 */

template <typename TElastix>
auto
AdvancedBSplineTransform<TElastix>::CreateDerivedTransformParameterMap() const -> ParameterMapType
{
  const auto gridRegion = m_BSplineTransform->GetGridRegion();

  return { { "GridSize", Conversion::ToVectorOfStrings(gridRegion.GetSize()) },
           { "GridIndex", Conversion::ToVectorOfStrings(gridRegion.GetIndex()) },
           { "GridSpacing", Conversion::ToVectorOfStrings(m_BSplineTransform->GetGridSpacing()) },
           { "GridOrigin", Conversion::ToVectorOfStrings(m_BSplineTransform->GetGridOrigin()) },
           { "GridDirection", Conversion::ToVectorOfStrings(m_BSplineTransform->GetGridDirection()) },
           { "BSplineTransformSplineOrder", { Conversion::ToString(m_SplineOrder) } },
           { "UseCyclicTransform", { Conversion::ToString(m_Cyclic) } } };

} // end CreateDerivedTransformParameterMap()


/**
 * *********************** SetOptimizerScales ***********************
 */

template <typename TElastix>
void
AdvancedBSplineTransform<TElastix>::SetOptimizerScales(const unsigned int edgeWidth)
{
  /** Some typedefs. */
  using ScalesValueType = itk::Optimizer::ScalesType::ValueType;

  /** Define new scales. */
  const NumberOfParametersType numberOfParameters = this->m_BSplineTransform->GetNumberOfParameters();
  const unsigned long          offset = numberOfParameters / SpaceDimension;
  itk::Optimizer::ScalesType   newScales(numberOfParameters, ScalesValueType{ 1.0 });
  const ScalesValueType        infScale = 10000.0;

  if (edgeWidth == 0)
  {
    /** Just set the unit scales into the optimizer. */
    this->m_Registration->GetAsITKBaseType()->GetModifiableOptimizer()->SetScales(newScales);
    return;
  }

  /** Get the grid region information and create a fake coefficient image. */
  RegionType   gridregion = this->m_BSplineTransform->GetGridRegion();
  SizeType     gridsize = gridregion.GetSize();
  IndexType    gridindex = gridregion.GetIndex();
  ImagePointer coeff = ImageType::New();
  coeff->SetRegions(gridregion);
  coeff->Allocate();

  /** Determine inset region. (so, the region with active parameters). */
  RegionType insetgridregion;
  SizeType   insetgridsize;
  IndexType  insetgridindex;
  for (unsigned int i = 0; i < SpaceDimension; ++i)
  {
    insetgridsize[i] = static_cast<unsigned int>(std::max(0, static_cast<int>(gridsize[i] - 2 * edgeWidth)));
    if (insetgridsize[i] == 0)
    {
      log::error(std::ostringstream{} << "ERROR: you specified a PassiveEdgeWidth of " << edgeWidth
                                      << ", while the total grid size in dimension " << i << " is only " << gridsize[i]
                                      << ".");
      itkExceptionMacro("ERROR: the PassiveEdgeWidth is too large!");
    }
    insetgridindex[i] = gridindex[i] + edgeWidth;
  }
  insetgridregion.SetSize(insetgridsize);
  insetgridregion.SetIndex(insetgridindex);

  /** Set up iterator over the coefficient image. */
  itk::ImageRegionExclusionConstIteratorWithIndex<ImageType> cIt(coeff, coeff->GetLargestPossibleRegion());
  cIt.SetExclusionRegion(insetgridregion);
  cIt.GoToBegin();

  /** Set the scales to infinity that correspond to edge coefficients
   * This (hopefully) makes sure they are not optimized during registration.
   */
  while (!cIt.IsAtEnd())
  {
    const IndexType &   index = cIt.GetIndex();
    const unsigned long baseOffset = coeff->ComputeOffset(index);
    for (unsigned int i = 0; i < SpaceDimension; ++i)
    {
      const auto scalesIndex = static_cast<unsigned int>(baseOffset + i * offset);
      newScales[scalesIndex] = infScale;
    }
    ++cIt;
  }

  /** Set the scales into the optimizer. */
  this->m_Registration->GetAsITKBaseType()->GetModifiableOptimizer()->SetScales(newScales);

} // end SetOptimizerScales()


} // end namespace elastix

#endif // end #ifndef elxAdvancedBSplineTransform_hxx
