/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  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.
 *
 *=========================================================================*/

//  Software Guide : BeginCommandLineArgs
//    INPUTS:  {BrainProtonDensitySliceBorder20.png}
//    INPUTS:  {BrainProtonDensitySliceR10X13Y17.png}
//    OUTPUTS: {ImageRegistration6Output.png}
//    OUTPUTS: {ImageRegistration6DifferenceBefore.png}
//    OUTPUTS: {ImageRegistration6DifferenceAfter.png}
//  Software Guide : EndCommandLineArgs


// Software Guide : BeginLatex
//
// This example illustrates the use of the \doxygen{Euler2DTransform}
// for performing registration. The example code is for the most part
// identical to the one presented in Section~\ref{sec:RigidRegistrationIn2D}.
// Even though this current example is done in $2D$, the class
// \doxygen{CenteredTransformInitializer} is quite generic and could be used
// in other dimensions. The objective of the initializer class is to simplify
// the computation of the center of rotation and the translation required to
// initialize certain transforms such as the
// Euler2DTransform. The initializer accepts two images and
// a transform as inputs. The images are considered to be the fixed and
// moving images of the registration problem, while the transform is the one
// used to register the images.
//
// The CenteredTransformInitializer supports two modes of operation. In the
// first mode, the centers of the images are computed as space coordinates
// using the image origin, size and spacing. The center of the fixed image is
// assigned as the rotational center of the transform while the vector going
// from the fixed image center to the moving image center is passed as the
// initial translation of the transform. In the second mode, the image centers
// are not computed geometrically but by using the moments of the intensity
// gray levels. The center of mass of each image is computed using the helper
// class \doxygen{ImageMomentsCalculator}.  The center of mass of the fixed
// image is passed as the rotational center of the transform while the vector
// going from the fixed image center of mass to the moving image center of
// mass is passed as the initial translation of the transform. This second
// mode of operation is quite convenient when the anatomical structures of
// interest are not centered in the image. In such cases the alignment of the
// centers of mass provides a better rough initial registration than the
// simple use of the geometrical centers.  The validity of the initial
// registration should be questioned when the two images are acquired in
// different imaging modalities. In those cases, the center of mass of
// intensities in one modality does not necessarily match the center of mass
// of intensities in the other imaging modality.
//
// \index{itk::Euler2DTransform}
// \index{itk::ImageMomentsCalculator}
//
//
// Software Guide : EndLatex

#include "itkImageRegistrationMethodv4.h"
#include "itkMeanSquaresImageToImageMetricv4.h"
#include "itkRegularStepGradientDescentOptimizerv4.h"


//  Software Guide : BeginLatex
//
//  The following are the most relevant headers in this example.
//
//  \index{itk::Euler2DTransform!header}
//
//  Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkEuler2DTransform.h"
#include "itkCenteredTransformInitializer.h"
// Software Guide : EndCodeSnippet


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

#include "itkResampleImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkSubtractImageFilter.h"


//
//  The following section of code implements a command observer
//  that will monitor the evolution of the registration process.
//
#include "itkCommand.h"
class CommandIterationUpdate : public itk::Command
{
public:
  using Self = CommandIterationUpdate;
  using Superclass = itk::Command;
  using Pointer = itk::SmartPointer<Self>;
  itkNewMacro(Self);

protected:
  CommandIterationUpdate() = default;

public:
  using OptimizerType = itk::RegularStepGradientDescentOptimizerv4<double>;
  using OptimizerPointer = const OptimizerType *;

  void
  Execute(itk::Object * caller, const itk::EventObject & event) override
  {
    Execute((const itk::Object *)caller, event);
  }

  void
  Execute(const itk::Object * object, const itk::EventObject & event) override
  {
    auto optimizer = static_cast<OptimizerPointer>(object);
    if (!itk::IterationEvent().CheckEvent(&event))
    {
      return;
    }
    std::cout << optimizer->GetCurrentIteration() << "   ";
    std::cout << optimizer->GetValue() << "   ";
    std::cout << optimizer->GetCurrentPosition() << std::endl;
  }
};

int
main(int argc, char * argv[])
{
  if (argc < 4)
  {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];
    std::cerr << " fixedImageFile  movingImageFile ";
    std::cerr << " outputImagefile  [differenceBeforeRegistration] ";
    std::cerr << " [differenceAfterRegistration] " << std::endl;
    return EXIT_FAILURE;
  }

  constexpr unsigned int Dimension = 2;
  using PixelType = float;

  using FixedImageType = itk::Image<PixelType, Dimension>;
  using MovingImageType = itk::Image<PixelType, Dimension>;


  //  Software Guide : BeginLatex
  //
  //  The transform type is instantiated using the code below. The only
  //  template parameter of this class is the representation type of the
  //  space coordinates.
  //
  //  \index{itk::Euler2DTransform!Instantiation}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using TransformType = itk::Euler2DTransform<double>;
  // Software Guide : EndCodeSnippet


  using OptimizerType = itk::RegularStepGradientDescentOptimizerv4<double>;
  using MetricType =
    itk::MeanSquaresImageToImageMetricv4<FixedImageType, MovingImageType>;
  using RegistrationType =
    itk::ImageRegistrationMethodv4<FixedImageType, MovingImageType>;

  MetricType::Pointer       metric = MetricType::New();
  OptimizerType::Pointer    optimizer = OptimizerType::New();
  RegistrationType::Pointer registration = RegistrationType::New();


  registration->SetMetric(metric);
  registration->SetOptimizer(optimizer);


  //  Software Guide : BeginLatex
  //
  //  Like the previous section, a direct initialization method is used here.
  //  The transform object is constructed below. This transform will
  //  be initialized, and its initial parameters will be considered as
  //  the parameters to be used when the registration process begins.
  //
  //  \index{itk::Euler2DTransform!Pointer}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  TransformType::Pointer transform = TransformType::New();
  // Software Guide : EndCodeSnippet

  using FixedImageReaderType = itk::ImageFileReader<FixedImageType>;
  using MovingImageReaderType = itk::ImageFileReader<MovingImageType>;
  FixedImageReaderType::Pointer fixedImageReader =
    FixedImageReaderType::New();
  MovingImageReaderType::Pointer movingImageReader =
    MovingImageReaderType::New();

  fixedImageReader->SetFileName(argv[1]);
  movingImageReader->SetFileName(argv[2]);


  registration->SetFixedImage(fixedImageReader->GetOutput());
  registration->SetMovingImage(movingImageReader->GetOutput());


  //  Software Guide : BeginLatex
  //
  //  The input images are taken from readers. It is not necessary to
  //  explicitly call \code{Update()} on the readers since the
  //  CenteredTransformInitializer class will do it as part of its
  //  initialization. The following code instantiates the initializer. This
  //  class is templated over the fixed and moving images type as well as the
  //  transform type. An initializer is then constructed by calling the
  //  \code{New()} method and assigning the result to a
  //  \doxygen{SmartPointer}.
  //
  // \index{itk::Euler2DTransform!Instantiation}
  // \index{itk::Euler2DTransform!New()}
  // \index{itk::Euler2DTransform!SmartPointer}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using TransformInitializerType =
    itk::CenteredTransformInitializer<TransformType,
                                      FixedImageType,
                                      MovingImageType>;

  TransformInitializerType::Pointer initializer =
    TransformInitializerType::New();
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  The initializer is now connected to the transform and to the fixed and
  //  moving images.
  //
  //  Software Guide : EndLatex


  // Software Guide : BeginCodeSnippet
  initializer->SetTransform(transform);
  initializer->SetFixedImage(fixedImageReader->GetOutput());
  initializer->SetMovingImage(movingImageReader->GetOutput());
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  The use of the geometrical centers is selected by calling
  //  \code{GeometryOn()} while the use of center of mass is selected by
  //  calling \code{MomentsOn()}.  Below we select the center of mass mode.
  //
  //  \index{CenteredTransformInitializer!MomentsOn()}
  //  \index{CenteredTransformInitializer!GeometryOn()}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  initializer->MomentsOn();
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Finally, the computation of the center and translation is triggered by
  //  the \code{InitializeTransform()} method. The resulting values will be
  //  passed directly to the transform.
  //
  //  Software Guide : EndLatex


  // Software Guide : BeginCodeSnippet
  initializer->InitializeTransform();
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  The remaining parameters of the transform are initialized as before.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  transform->SetAngle(0.0);
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Now the initialized transform object will be set to the registration
  //  method, and the starting point of the registration is defined by its
  //  initial parameters.
  //
  //  If the \code{InPlaceOn()} method is called, this initialized transform
  //  will be the output transform object or ``grafted'' to the output.
  //  Otherwise, this
  //  ``InitialTransform'' will be deep-copied or
  //  ``cloned'' to the output.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  registration->SetInitialTransform(transform);
  registration->InPlaceOn();
  // Software Guide : EndCodeSnippet


  using OptimizerScalesType = OptimizerType::ScalesType;
  OptimizerScalesType optimizerScales(transform->GetNumberOfParameters());
  const double        translationScale = 1.0 / 1000.0;

  optimizerScales[0] = 1.0;
  optimizerScales[1] = translationScale;
  optimizerScales[2] = translationScale;

  optimizer->SetScales(optimizerScales);

  optimizer->SetLearningRate(0.1);
  optimizer->SetMinimumStepLength(0.001);
  optimizer->SetNumberOfIterations(200);


  // Create the Command observer and register it with the optimizer.
  //
  CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
  optimizer->AddObserver(itk::IterationEvent(), observer);

  // One level registration process without shrinking and smoothing.
  //
  constexpr unsigned int numberOfLevels = 1;

  RegistrationType::ShrinkFactorsArrayType shrinkFactorsPerLevel;
  shrinkFactorsPerLevel.SetSize(1);
  shrinkFactorsPerLevel[0] = 1;

  RegistrationType::SmoothingSigmasArrayType smoothingSigmasPerLevel;
  smoothingSigmasPerLevel.SetSize(1);
  smoothingSigmasPerLevel[0] = 0;

  registration->SetNumberOfLevels(numberOfLevels);
  registration->SetSmoothingSigmasPerLevel(smoothingSigmasPerLevel);
  registration->SetShrinkFactorsPerLevel(shrinkFactorsPerLevel);

  try
  {
    registration->Update();
    std::cout << "Optimizer stop condition: "
              << registration->GetOptimizer()->GetStopConditionDescription()
              << std::endl;
  }
  catch (const itk::ExceptionObject & err)
  {
    std::cerr << "ExceptionObject caught !" << std::endl;
    std::cerr << err << std::endl;
    return EXIT_FAILURE;
  }


  //  Software Guide : BeginLatex
  //
  //  Since the registration filter has \code{InPlace} set, the transform
  //  object is grafted to the output and is updated by the registration
  //  method.
  //
  //  Software Guide : EndLatex

  TransformType::ParametersType finalParameters = transform->GetParameters();


  const double finalAngle = finalParameters[0];
  const double finalTranslationX = finalParameters[1];
  const double finalTranslationY = finalParameters[2];

  const double rotationCenterX =
    registration->GetOutput()->Get()->GetFixedParameters()[0];
  const double rotationCenterY =
    registration->GetOutput()->Get()->GetFixedParameters()[1];

  const unsigned int numberOfIterations = optimizer->GetCurrentIteration();
  const double       bestValue = optimizer->GetValue();

  // Print out results
  //
  const double finalAngleInDegrees = finalAngle * 180.0 / itk::Math::pi;

  std::cout << "Result = " << std::endl;
  std::cout << " Angle (radians) " << finalAngle << std::endl;
  std::cout << " Angle (degrees)  " << finalAngleInDegrees << std::endl;
  std::cout << " Translation X  = " << finalTranslationX << std::endl;
  std::cout << " Translation Y  = " << finalTranslationY << std::endl;
  std::cout << " Fixed Center X = " << rotationCenterX << std::endl;
  std::cout << " Fixed Center Y = " << rotationCenterY << std::endl;
  std::cout << " Iterations     = " << numberOfIterations << std::endl;
  std::cout << " Metric value   = " << bestValue << std::endl;


  //  Software Guide : BeginLatex
  //
  //  Let's execute this example over some of the images provided in
  //  \code{Examples/Data}, for example:
  //
  //  \begin{itemize}
  //  \item \code{BrainProtonDensitySliceBorder20.png}
  //  \item \code{BrainProtonDensitySliceR10X13Y17.png}
  //  \end{itemize}
  //
  //  The second image is the result of intentionally rotating the first
  //  image by $10$ degrees around the geometric center and shifting
  //  it $13mm$ in $X$ and $17mm$ in $Y$. Both images have
  //  unit-spacing and are shown in Figure
  //  \ref{fig:FixedMovingImageRegistration5}. The registration takes
  //  $21$ iterations and produces:
  //
  //  \begin{center}
  //  \begin{verbatim}
  //  [ 0.174527, 12.4528, 16.0766]
  //  \end{verbatim}
  //  \end{center}
  //
  //  These parameters are interpreted as
  //
  //  \begin{itemize}
  //  \item Angle         =                  $0.174527$     radians
  //  \item Translation   = $( 12.4528, 16.0766 )$ millimeters
  //  \end{itemize}
  //
  //  Note that the reported translation is not the translation of $(13,17)$
  //  that might be expected. The reason is that we used the center of
  //  mass $( 111.204, 131.591 )$  for the fixed center, while the input was
  //  rotated about the geometric center $( 110.5, 128.5 )$.  It is more
  //  illustrative in this case to take a look at the actual rotation matrix
  //  and offset resulting from the five parameters.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  TransformType::MatrixType matrix = transform->GetMatrix();
  TransformType::OffsetType offset = transform->GetOffset();

  std::cout << "Matrix = " << std::endl << matrix << std::endl;
  std::cout << "Offset = " << std::endl << offset << std::endl;
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  Which produces the following output.
  //
  //  \begin{verbatim}
  //  Matrix =
  //     0.984809 -0.173642
  //     0.173642 0.984809
  //
  //  Offset =
  //     [36.9919, -1.23402]
  //  \end{verbatim}
  //
  //  This output illustrates how counter-intuitive the mix of center of
  //  rotation and translations can be. Figure
  //  \ref{fig:TranslationAndRotationCenter} will clarify this situation. The
  //  figure shows the original image on the left. A rotation of $10^{\circ}$
  //  around the center of the image is shown in the middle. The same rotation
  //  performed around the origin of coordinates is shown on the right. It can
  //  be seen here that changing the center of rotation introduces additional
  //  translations.
  //
  //  Let's analyze what happens to the center of the image that we just
  //  registered. Under the point of view of rotating $10^{\circ}$ around the
  //  center and then applying a translation of $(13mm,17mm)$. The image has
  //  a size of $(221 \times 257)$ pixels and unit spacing. Hence its center
  //  has coordinates $(110.5,128.5)$. Since the rotation is done around this
  //  point, the center behaves as the fixed point of the transformation and
  //  remains unchanged. Then with the $(13mm,17mm)$ translation it is mapped
  //  to $(123.5,145.5)$ which becomes its final position.
  //
  //  The matrix and offset that we obtained at the end of the registration
  //  indicate that this should be equivalent to a rotation of $10^{\circ}$
  //  around the origin, followed by a translation of $(36.99, -1.23)$. Let's
  //  compute this in detail. First the rotation of the image center by
  //  $10^{\circ}$ around the origin will move the point
  //  $(110.5,128.5)$ to $(86.51,145.74)$. Now, applying a translation
  //  of $(36.99,-1.23)$ maps this point to $(123.50, 144.50)$, which
  //  is very close to the result of our previous computation.
  //
  //  It is unlikely that we could have chosen these translations as the
  //  initial guess, since we tend to think about images in a coordinate
  //  system whose origin is in the center of the image.
  //
  // \begin{figure}
  // \center
  // \includegraphics[width=\textwidth]{TranslationAndRotationCenter}
  // \itkcaption[Effect of changing the center of rotation]{Effect of changing
  // the center of rotation.}
  // \label{fig:TranslationAndRotationCenter}
  // \end{figure}
  //
  //  Software Guide : EndLatex


  //  Software Guide : BeginLatex
  //
  //  This underscores the importance of using good initialization for
  //  the center for a transform fixed parameter. By using either the
  //  center of geometry or center of mass for initialization the
  //  rotation and translation parameters may have a more intuitive
  //  interpretation than if only the optimization parameters of
  //  translation and rotation are initialized.
  //
  //  Software Guide : EndLatex


  //  Software Guide : BeginLatex
  //
  // \begin{figure}
  // \center
  // \includegraphics[width=0.44\textwidth]{BrainProtonDensitySliceBorder20}
  // \includegraphics[width=0.44\textwidth]{BrainProtonDensitySliceR10X13Y17}
  // \itkcaption[CenteredTransformInitializer input images]{Fixed and moving
  // images provided as input to the registration method using
  // CenteredTransformInitializer.}
  // \label{fig:FixedMovingImageRegistration6}
  // \end{figure}
  //
  //
  // \begin{figure}
  // \center
  // \includegraphics[width=0.32\textwidth]{ImageRegistration6Output}
  // \includegraphics[width=0.32\textwidth]{ImageRegistration6DifferenceBefore}
  // \includegraphics[width=0.32\textwidth]{ImageRegistration6DifferenceAfter}
  // \itkcaption[CenteredTransformInitializer output images]{Resampled moving
  // image (left). Differences between fixed and moving images, before
  // registration (center) and after registration (right) with the
  // CenteredTransformInitializer.}
  // \label{fig:ImageRegistration6Outputs}
  // \end{figure}
  //
  // Figure \ref{fig:ImageRegistration6Outputs} shows the output of the
  // registration. The image on the right of this figure shows the differences
  // between the fixed image and the resampled moving image after
  // registration.
  //
  // \begin{figure}
  // \center
  // \includegraphics[height=0.32\textwidth]{ImageRegistration6TraceMetric}
  // \includegraphics[height=0.32\textwidth]{ImageRegistration6TraceAngle}
  // \includegraphics[height=0.32\textwidth]{ImageRegistration6TraceTranslations}
  // \itkcaption[CenteredTransformInitializer output plots]{Plots of the
  // Metric, rotation angle, center of rotation and translations during the
  // registration using CenteredTransformInitializer.}
  // \label{fig:ImageRegistration6Plots}
  // \end{figure}
  //
  //  Figure \ref{fig:ImageRegistration6Plots} plots the output parameters of
  //  the registration process. It includes the metric values at every
  //  iteration, the angle values at every iteration, and the values of the
  //  translation components as the registration progresses. Note that this is
  //  the complementary translation as used in the transform, not the actual
  //  total translation that is used in the transform offset. We could modify
  //  the observer to print the total offset instead of printing the array of
  //  parameters. Let's call that an exercise for the reader!
  //
  //  Software Guide : EndLatex


  using ResampleFilterType =
    itk::ResampleImageFilter<MovingImageType, FixedImageType>;
  ResampleFilterType::Pointer resample = ResampleFilterType::New();

  resample->SetTransform(transform);
  resample->SetInput(movingImageReader->GetOutput());

  FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();

  resample->SetSize(fixedImage->GetLargestPossibleRegion().GetSize());
  resample->SetOutputOrigin(fixedImage->GetOrigin());
  resample->SetOutputSpacing(fixedImage->GetSpacing());
  resample->SetOutputDirection(fixedImage->GetDirection());
  resample->SetDefaultPixelValue(100);

  using OutputPixelType = unsigned char;

  using OutputImageType = itk::Image<OutputPixelType, Dimension>;

  using CastFilterType =
    itk::CastImageFilter<FixedImageType, OutputImageType>;

  using WriterType = itk::ImageFileWriter<OutputImageType>;


  WriterType::Pointer     writer = WriterType::New();
  CastFilterType::Pointer caster = CastFilterType::New();


  writer->SetFileName(argv[3]);


  caster->SetInput(resample->GetOutput());
  writer->SetInput(caster->GetOutput());
  writer->Update();

  // Now compute the difference between the images
  // before and after registration.
  //
  using DifferenceImageType = itk::Image<float, Dimension>;

  using DifferenceFilterType = itk::
    SubtractImageFilter<FixedImageType, FixedImageType, DifferenceImageType>;

  DifferenceFilterType::Pointer difference = DifferenceFilterType::New();

  using OutputPixelType = unsigned char;

  using OutputImageType = itk::Image<OutputPixelType, Dimension>;

  using RescalerType =
    itk::RescaleIntensityImageFilter<DifferenceImageType, OutputImageType>;

  RescalerType::Pointer intensityRescaler = RescalerType::New();

  intensityRescaler->SetOutputMinimum(0);
  intensityRescaler->SetOutputMaximum(255);

  difference->SetInput1(fixedImageReader->GetOutput());
  difference->SetInput2(resample->GetOutput());

  resample->SetDefaultPixelValue(1);

  intensityRescaler->SetInput(difference->GetOutput());

  using WriterType = itk::ImageFileWriter<OutputImageType>;

  WriterType::Pointer writer2 = WriterType::New();

  writer2->SetInput(intensityRescaler->GetOutput());


  try
  {
    // Compute the difference image between the
    // fixed and moving image after registration.
    if (argc > 5)
    {
      writer2->SetFileName(argv[5]);
      writer2->Update();
    }

    // Compute the difference image between the
    // fixed and resampled moving image after registration.
    TransformType::Pointer identityTransform = TransformType::New();
    identityTransform->SetIdentity();
    resample->SetTransform(identityTransform);
    if (argc > 4)
    {
      writer2->SetFileName(argv[4]);
      writer2->Update();
    }
  }
  catch (const itk::ExceptionObject & excp)
  {
    std::cerr << "Error while writing difference images" << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
  }

  return EXIT_SUCCESS;
}