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 *
 *  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 : BeginLatex
//
// This example illustrates how to explore the domain of an image metric. This
// is a useful exercise before starting a registration process, since
// familiarity with the characteristics of the metric is fundamental for
// appropriate selection of the optimizer and its parameters used to drive the
// registration process.
// This process helps identify how noisy a metric may be in a given
// range of parameters, and it will also give an idea of the number of local
// minima or maxima in which an optimizer may get trapped while exploring the
// parametric space.
//
// Software Guide : EndLatex


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


// Software Guide : BeginLatex
//
// We start by including the headers of the basic components: Metric,
// Transform and Interpolator.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkMeanSquaresImageToImageMetricv4.h"
#include "itkTranslationTransform.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
// Software Guide : EndCodeSnippet


int
main(int argc, char * argv[])
{
  if (argc < 3)
  {
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0] << "  fixedImage  movingImage" << std::endl;
    return EXIT_FAILURE;
  }

  // Software Guide : BeginLatex
  //
  // We define the dimension and pixel type of the images to be used in the
  // evaluation of the Metric.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  constexpr unsigned int Dimension = 2;
  using PixelType = float;

  using ImageType = itk::Image<PixelType, Dimension>;
  // Software Guide : EndCodeSnippet


  using ReaderType = itk::ImageFileReader<ImageType>;

  ReaderType::Pointer fixedReader = ReaderType::New();
  ReaderType::Pointer movingReader = ReaderType::New();

  fixedReader->SetFileName(argv[1]);
  movingReader->SetFileName(argv[2]);

  try
  {
    fixedReader->Update();
    movingReader->Update();
  }
  catch (const itk::ExceptionObject & excep)
  {
    std::cerr << "Exception catched !" << std::endl;
    std::cerr << excep << std::endl;
  }

  // Software Guide : BeginLatex
  //
  // The type of the Metric is instantiated and one is constructed.  In this
  // case we decided to use the same image type for both the fixed and the
  // moving images.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using MetricType =
    itk::MeanSquaresImageToImageMetricv4<ImageType, ImageType>;

  MetricType::Pointer metric = MetricType::New();
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // We also instantiate the transform and interpolator types, and create
  // objects of each class.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using TransformType = itk::TranslationTransform<double, Dimension>;

  TransformType::Pointer transform = TransformType::New();


  using InterpolatorType =
    itk::NearestNeighborInterpolateImageFunction<ImageType, double>;

  InterpolatorType::Pointer interpolator = InterpolatorType::New();
  // Software Guide : EndCodeSnippet


  transform->SetIdentity();

  ImageType::ConstPointer fixedImage = fixedReader->GetOutput();
  ImageType::ConstPointer movingImage = movingReader->GetOutput();


  // Software Guide : BeginLatex
  //
  // The classes required by the metric are connected to it. This includes the
  // fixed and moving images, the interpolator and the transform.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  metric->SetTransform(transform);
  metric->SetMovingInterpolator(interpolator);

  metric->SetFixedImage(fixedImage);
  metric->SetMovingImage(movingImage);
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Note that the \code{SetTransform()} method is equivalent to the
  // \code{SetMovingTransform()} function. In this example there is
  // no need to use the \code{SetFixedTransform()}, since the virtual
  // domain is assumed to be the same as the fixed image domain set
  // as following.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  metric->SetVirtualDomainFromImage(fixedImage);
  // Software Guide : EndCodeSnippet

  try
  {
    metric->Initialize();
  }
  catch (const itk::ExceptionObject & excep)
  {
    std::cerr << "Exception catched !" << std::endl;
    std::cerr << excep << std::endl;
    return EXIT_FAILURE;
  }


  // Software Guide : BeginLatex
  //
  // Finally we select a region of the parametric space to explore. In this
  // case we are using a translation transform in 2D, so we simply select
  // translations from a negative position to a positive position, in both $x$
  // and $y$. For each one of those positions we invoke the \code{GetValue()}
  // method of the Metric.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  MetricType::MovingTransformParametersType displacement(Dimension);

  constexpr int rangex = 50;
  constexpr int rangey = 50;

  for (int dx = -rangex; dx <= rangex; dx++)
  {
    for (int dy = -rangey; dy <= rangey; dy++)
    {
      displacement[0] = dx;
      displacement[1] = dy;
      metric->SetParameters(displacement);
      const double value = metric->GetValue();
      std::cout << dx << "   " << dy << "   " << value << std::endl;
    }
  }
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // \begin{figure}
  // \center
  // \includegraphics[height=0.33\textwidth]{MeanSquaresMetricPlot1}
  // \includegraphics[height=0.33\textwidth]{MeanSquaresMetricPlot2}
  // \itkcaption[Mean Squares Metric Plots]{Plots of the Mean Squares Metric
  // for an image compared to itself under multiple translations.}
  // \label{fig:MeanSquaresMetricPlot}
  // \end{figure}
  //
  // Running this code using the image BrainProtonDensitySlice.png as both the
  // fixed and the moving images results in the plot shown in
  // Figure~\ref{fig:MeanSquaresMetricPlot}. From this figure, it can be seen
  // that a gradient-based optimizer will be appropriate for finding the
  // extrema of the Metric. It is also possible to estimate a good value for
  // the step length of a gradient-descent optimizer.
  //
  // This exercise of plotting the Metric is probably the best thing to do
  // when a registration process is not converging and when it is unclear how
  // to fine tune the different parameters involved in the registration. This
  // includes the optimizer parameters, the metric parameters and even options
  // such as preprocessing the image data with smoothing filters.
  //
  // The shell and Gnuplot\footnote{http://www.gnuplot.info} scripts used for
  // generating the graphics in Figure~\ref{fig:MeanSquaresMetricPlot} are
  // available in the directory
  //
  //             \code{ITKSoftwareGuide/SoftwareGuide/Art}
  //
  // Of course, this plotting exercise becomes more challenging when the
  // transform has more than three parameters, and when those parameters have
  // very different value ranges. In those cases it is necessary to select
  // only a key subset of parameters from the transform and to study the
  // behavior of the metric when those parameters are varied.
  //
  //
  // Software Guide : EndLatex


  return EXIT_SUCCESS;
}