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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 : BeginCommandLineArgs
//    INPUTS:  {BrainT1Slice.png}
//    INPUTS:  {BrainT1Slice_labelled.png}
//    OUTPUTS: {ScalarImageMarkovRandomField1Output.png}
//    ARGUMENTS:    50 3 3 14.8 91.6 134.9
//  Software Guide : EndCommandLineArgs

// Software Guide : BeginLatex
//
// This example shows how to use the Markov Random Field approach for
// classifying the pixel of a scalar image.
//
// The  \subdoxygen{Statistics}{MRFImageFilter} is used for refining an
// initial classification by introducing the spatial coherence of the labels.
// The user should provide two images as input. The first image is the one to
// be classified while the second image is an image of labels representing an
// initial classification.
//
// Software Guide : EndLatex


// Software Guide : BeginLatex
//
// The following headers are related to reading input images, writing the
// output image, and making the necessary conversions between scalar and
// vector images.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkComposeImageFilter.h"
// Software Guide : EndCodeSnippet

#include "itkRescaleIntensityImageFilter.h"

// Software Guide : BeginLatex
//
// The following headers are related to the statistical classification
// classes.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkMRFImageFilter.h"
#include "itkDistanceToCentroidMembershipFunction.h"
#include "itkMinimumDecisionRule.h"
// Software Guide : EndCodeSnippet

int
main(int argc, char * argv[])
{
  if (argc < 7)
  {
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0];
    std::cerr << " inputScalarImage inputLabeledImage";
    std::cerr << " outputLabeledImage numberOfIterations";
    std::cerr << " smoothingFactor numberOfClasses";
    std::cerr << " mean1 mean2 ... meanN " << std::endl;
    return EXIT_FAILURE;
  }

  const char * inputImageFileName = argv[1];
  const char * inputLabelImageFileName = argv[2];
  const char * outputImageFileName = argv[3];

  const unsigned int numberOfIterations = std::stoi(argv[4]);
  const double       smoothingFactor = std::stod(argv[5]);
  const unsigned int numberOfClasses = std::stoi(argv[6]);

  constexpr unsigned int numberOfArgumentsBeforeMeans = 7;

  if (static_cast<unsigned int>(argc) <
      numberOfClasses + numberOfArgumentsBeforeMeans)
  {
    std::cerr << "Error: " << std::endl;
    std::cerr << numberOfClasses << " classes have been specified ";
    std::cerr << "but not enough means have been provided in the command ";
    std::cerr << "line arguments " << std::endl;
    return EXIT_FAILURE;
  }


  // Software Guide : BeginLatex
  //
  // First we define the pixel type and dimension of the image that we intend
  // to classify. With this image type we can also declare the
  // \doxygen{ImageFileReader} needed for reading the input image, create one
  // and set its input filename. In this particular case we choose to use
  // \code{signed short} as pixel type, which is typical for MicroMRI and CT
  // data sets.
  //
  // Software Guide : EndLatex

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

  using ImageType = itk::Image<PixelType, Dimension>;

  using ReaderType = itk::ImageFileReader<ImageType>;
  ReaderType::Pointer reader = ReaderType::New();
  reader->SetFileName(inputImageFileName);
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // As a second step we define the pixel type and dimension of the image of
  // labels that provides the initial classification of the pixels from the
  // first image. This initial labeled image can be the output of a K-Means
  // method like the one illustrated in section \ref{sec:KMeansClassifier}.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using LabelPixelType = unsigned char;

  using LabelImageType = itk::Image<LabelPixelType, Dimension>;

  using LabelReaderType = itk::ImageFileReader<LabelImageType>;
  LabelReaderType::Pointer labelReader = LabelReaderType::New();
  labelReader->SetFileName(inputLabelImageFileName);
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // Since the Markov Random Field algorithm is defined in general for images
  // whose pixels have multiple components, that is, images of vector type, we
  // must adapt our scalar image in order to satisfy the interface expected by
  // the \code{MRFImageFilter}. We do this by using the
  // \doxygen{ComposeImageFilter}. With this filter we will present our
  // scalar image as a vector image whose vector pixels contain a single
  // component.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using ArrayPixelType = itk::FixedArray<LabelPixelType, 1>;

  using ArrayImageType = itk::Image<ArrayPixelType, Dimension>;

  using ScalarToArrayFilterType =
    itk::ComposeImageFilter<ImageType, ArrayImageType>;

  ScalarToArrayFilterType::Pointer scalarToArrayFilter =
    ScalarToArrayFilterType::New();
  scalarToArrayFilter->SetInput(reader->GetOutput());
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // With the input image type \code{ImageType} and labeled image type
  // \code{LabelImageType} we instantiate the type of the
  // \doxygen{MRFImageFilter} that will apply the Markov Random Field
  // algorithm in order to refine the pixel classification.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using MRFFilterType = itk::MRFImageFilter<ArrayImageType, LabelImageType>;

  MRFFilterType::Pointer mrfFilter = MRFFilterType::New();

  mrfFilter->SetInput(scalarToArrayFilter->GetOutput());
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // We set now some of the parameters for the MRF filter. In particular, the
  // number of classes to be used during the classification, the maximum
  // number of iterations to be run in this filter and the error tolerance
  // that will be used as a criterion for convergence.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  mrfFilter->SetNumberOfClasses(numberOfClasses);
  mrfFilter->SetMaximumNumberOfIterations(numberOfIterations);
  mrfFilter->SetErrorTolerance(1e-7);
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // The smoothing factor represents the tradeoff between fidelity to the
  // observed image and the smoothness of the segmented image. Typical
  // smoothing factors have values between 1~5. This factor will multiply the
  // weights that define the influence of neighbors on the classification of a
  // given pixel. The higher the value, the more uniform will be the regions
  // resulting from the classification refinement.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  mrfFilter->SetSmoothingFactor(smoothingFactor);
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // Given that the MRF filter need to continually relabel the pixels, it
  // needs access to a set of membership functions that will measure to what
  // degree every pixel belongs to a particular class.  The classification is
  // performed by the \doxygen{ImageClassifierBase} class, that is
  // instantiated using the type of the input vector image and the type of the
  // labeled image.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using SupervisedClassifierType =
    itk::ImageClassifierBase<ArrayImageType, LabelImageType>;

  SupervisedClassifierType::Pointer classifier =
    SupervisedClassifierType::New();
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // The classifier need a decision rule to be set by the user. Note that we
  // must use \code{GetPointer()} in the call of the \code{SetDecisionRule()}
  // method because we are passing a SmartPointer, and smart pointer cannot
  // perform polymorphism, we must then extract the raw pointer that is
  // associated to the smart pointer. This extraction is done with the
  // GetPointer() method.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using DecisionRuleType = itk::Statistics::MinimumDecisionRule;

  DecisionRuleType::Pointer classifierDecisionRule = DecisionRuleType::New();

  classifier->SetDecisionRule(classifierDecisionRule);
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // We now instantiate the membership functions. In this case we use the
  // \subdoxygen{Statistics}{DistanceToCentroidMembershipFunction} class
  // templated over the pixel type of the vector image, that in our example
  // happens to be a vector of dimension 1.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using MembershipFunctionType =
    itk::Statistics::DistanceToCentroidMembershipFunction<ArrayPixelType>;

  using MembershipFunctionPointer = MembershipFunctionType::Pointer;


  double                               meanDistance = 0;
  MembershipFunctionType::CentroidType centroid(1);
  for (unsigned int i = 0; i < numberOfClasses; i++)
  {
    MembershipFunctionPointer membershipFunction =
      MembershipFunctionType::New();

    centroid[0] = std::stod(argv[i + numberOfArgumentsBeforeMeans]);

    membershipFunction->SetCentroid(centroid);

    classifier->AddMembershipFunction(membershipFunction);
    meanDistance += static_cast<double>(centroid[0]);
  }
  if (numberOfClasses > 0)
  {
    meanDistance /= numberOfClasses;
  }
  else
  {
    std::cerr << "ERROR: numberOfClasses is 0" << std::endl;
    return EXIT_FAILURE;
  }
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // We set the Smoothing factor. This factor will multiply the weights that
  // define the influence of neighbors on the classification of a given pixel.
  // The higher the value, the more uniform will be the regions resulting from
  // the classification refinement.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  mrfFilter->SetSmoothingFactor(smoothingFactor);
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // and we set the neighborhood radius that will define the size of the
  // clique to be used in the computation of the neighbors' influence in the
  // classification of any given pixel. Note that despite the fact that we
  // call this a radius, it is actually the half size of an hypercube. That
  // is, the actual region of influence will not be circular but rather an
  // N-Dimensional box. For example, a neighborhood radius of 2 in a 3D image
  // will result in a clique of size 5x5x5 pixels, and a radius of 1 will
  // result in a clique of size 3x3x3 pixels.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  mrfFilter->SetNeighborhoodRadius(1);
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // We should now set the weights used for the neighbors. This is done by
  // passing an array of values that contains the linear sequence of weights
  // for the neighbors. For example, in a neighborhood of size 3x3x3, we
  // should provide a linear array of 9 weight values. The values are packaged
  // in a \code{std::vector} and are supposed to be \code{double}. The
  // following lines illustrate a typical set of values for a 3x3x3
  // neighborhood. The array is arranged and then passed to the filter by
  // using the method \code{SetMRFNeighborhoodWeight()}.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  std::vector<double> weights;
  weights.push_back(1.5);
  weights.push_back(2.0);
  weights.push_back(1.5);
  weights.push_back(2.0);
  weights.push_back(0.0); // This is the central pixel
  weights.push_back(2.0);
  weights.push_back(1.5);
  weights.push_back(2.0);
  weights.push_back(1.5);
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // We now scale weights so that the smoothing function and the image
  // fidelity functions have comparable value. This is necessary since the
  // label image and the input image can have different dynamic ranges. The
  // fidelity function is usually computed using a distance function, such as
  // the \doxygen{DistanceToCentroidMembershipFunction} or one of the other
  // membership functions. They tend to have values in the order of the means
  // specified.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  double totalWeight = 0;
  for (double weight : weights)
  {
    totalWeight += weight;
  }
  for (double & weight : weights)
  {
    weight = static_cast<double>(weight * meanDistance / (2 * totalWeight));
  }

  mrfFilter->SetMRFNeighborhoodWeight(weights);
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // Finally, the classifier class is connected to the Markof Random Fields
  // filter.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  mrfFilter->SetClassifier(classifier);
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // The output image produced by the \doxygen{MRFImageFilter} has the same
  // pixel type as the labeled input image. In the following lines we use the
  // \code{OutputImageType} in order to instantiate the type of a
  // \doxygen{ImageFileWriter}. Then create one, and connect it to the output
  // of the classification filter after passing it through an intensity
  // rescaler to rescale it to an 8 bit dynamic range
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using OutputImageType = MRFFilterType::OutputImageType;
  // Software Guide : EndCodeSnippet

  // Rescale outputs to the dynamic range of the display
  using RescaledOutputImageType = itk::Image<unsigned char, Dimension>;
  using RescalerType =
    itk::RescaleIntensityImageFilter<OutputImageType,
                                     RescaledOutputImageType>;

  RescalerType::Pointer intensityRescaler = RescalerType::New();
  intensityRescaler->SetOutputMinimum(0);
  intensityRescaler->SetOutputMaximum(255);
  intensityRescaler->SetInput(mrfFilter->GetOutput());

  // Software Guide : BeginCodeSnippet
  using WriterType = itk::ImageFileWriter<OutputImageType>;

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

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

  writer->SetFileName(outputImageFileName);
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // We are now ready for triggering the execution of the pipeline. This is
  // done by simply invoking the \code{Update()} method in the writer. This
  // call will propagate the update request to the reader and then to the MRF
  // filter.
  //
  // Software Guide : EndLatex


  // Software Guide : BeginCodeSnippet
  try
  {
    writer->Update();
  }
  catch (const itk::ExceptionObject & excp)
  {
    std::cerr << "Problem encountered while writing ";
    std::cerr << " image file : " << argv[2] << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
  }
  // Software Guide : EndCodeSnippet

  std::cout << "Number of Iterations : ";
  std::cout << mrfFilter->GetNumberOfIterations() << std::endl;
  std::cout << "Stop condition: " << std::endl;
  std::cout << "  (1) Maximum number of iterations " << std::endl;
  std::cout << "  (2) Error tolerance:  " << std::endl;
  std::cout << mrfFilter->GetStopCondition() << std::endl;

  //  Software Guide : BeginLatex
  //
  // \begin{figure} \center
  // \includegraphics[width=0.44\textwidth]{ScalarImageMarkovRandomField1Output}
  // \itkcaption[Output of the ScalarImageMarkovRandomField]{Effect of the
  // MRF filter on a T1 slice of the brain.}
  // \label{fig:ScalarImageMarkovRandomFieldInputOutput}
  // \end{figure}
  //
  //  Figure \ref{fig:ScalarImageMarkovRandomFieldInputOutput}
  //  illustrates the effect of this filter with three classes.
  //  In this example the filter was run with a smoothing factor of 3.
  //  The labeled image was produced by ScalarImageKmeansClassifier.cxx
  //  and the means were estimated by ScalarImageKmeansModelEstimator.cxx.
  //
  //  Software Guide : EndLatex

  return EXIT_SUCCESS;
}