/*=========================================================================
 *
 *  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
 *
 *         https://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
//
// In medical imaging applications, the general shape, location and
// orientation of an anatomical structure of interest is typically
// known \emph{a priori}. This information can be used to aid the
// segmentation process especially when image contrast is low or
// when the object boundary is not distinct.
//
// In \cite{Leventon2000}, Leventon \emph{et al.} extended the
// geodesic active contours method with an additional shape-influenced term in
// the driving PDE. The
// \doxygen{GeodesicActiveContourShapePriorLevelSetImageFilter} is a
// generalization of Leventon's approach and its use is illustrated in the
// following example.
//
// To support shape-guidance, the generic level set
// equation (Eqn(~\ref{eqn:LevelSetEquation})) is extended to incorporate a
// shape guidance term:
//
// \begin{equation}
// \label{eqn:ShapeInfluenceTerm}
// \xi \left(\psi^{*}(\mathbf{x}) - \psi(\mathbf{x})\right)
// \end{equation}
//
// where $\psi^{*}$ is the signed distance function of the ``best-fit'' shape
// with respect to a shape model. The new term has the effect of driving the
// contour towards the best-fit shape. The scalar $\xi$ weights the influence
// of the shape term in the overall evolution. In general, the best-fit shape
// is not known ahead of time and has to be iteratively estimated in
// conjunction with the contour evolution.
//
// As with the \doxygen{GeodesicActiveContourLevelSetImageFilter}, the
// GeodesicActiveContourShapePriorLevelSetImageFilter expects two input
// images: the first is an initial level set and the second a feature image
// that represents the image edge potential. The configuration of this
// example is quite similar to the example in
// Section~\ref{sec:GeodesicActiveContourImageFilter} and hence the
// description will focus on the new objects involved in the segmentation
// process as shown in
// Figure~\ref{fig:GeodesicActiveContourShapePriorCollaborationDiagram}.
//
// \begin{figure} \center
// \includegraphics[width=\textwidth]{GeodesicActiveContourShapePriorCollaborationDiagram}
// \itkcaption[GeodesicActiveContourShapePriorLevelSetImageFilter
// collaboration diagram]{Collaboration diagram for the
// GeodesicActiveContourShapePriorLevelSetImageFilter applied to a
// segmentation task.}
// \label{fig:GeodesicActiveContourShapePriorCollaborationDiagram}
// \end{figure}
//
// The process pipeline begins with centering the input image using the
// the \doxygen{ChangeInformationImageFilter} to simplify the estimation of
// the pose of the shape, to be explained later. The centered image is then
// smoothed using non-linear diffusion to remove noise and the gradient
// magnitude is computed from the smoothed image. For simplicity, this example
// uses the \doxygen{BoundedReciprocalImageFilter} to produce the edge
// potential image.
//
// The \doxygen{FastMarchingImageFilter} creates an initial level set using
// three user specified seed positions and an initial contour radius. Three
// seeds are used in this example to facilitate the segmentation of long
// narrow objects in a smaller number of iterations. The output of the
// FastMarchingImageFilter is passed as the input to the
// GeodesicActiveContourShapePriorLevelSetImageFilter. At then end of the
// segmentation process, the output level set is passed to the
// \doxygen{BinaryThresholdImageFilter} to produce a binary mask representing
// the segmented object.
//
// The remaining objects in
// Figure~\ref{fig:GeodesicActiveContourShapePriorCollaborationDiagram}
// are used for shape modeling and estimation.
// The \doxygen{PCAShapeSignedDistanceFunction} represents a statistical
// shape model defined by a mean signed distance and the first $K$
// principal components modes; while the \doxygen{Euler2DTransform} is used
// to represent the pose of the shape. In this implementation, the
// best-fit shape estimation problem is reformulated as a minimization problem
// where the \doxygen{ShapePriorMAPCostFunction} is the cost function to
// be optimized using the \doxygen{OnePlusOneEvolutionaryOptimizer}.
//
// It should be noted that, although particular shape model, transform
// cost function, and optimizer are used in this example, the implementation
// is generic, allowing different instances of these components to be
// plugged in. This flexibility allows a user to tailor the behavior of the
// segmentation process to suit the circumstances of the targeted application.
//
// Let's start the example by including the headers of the new filters
// involved in the segmentation.
//
// Software Guide : EndLatex


// Software Guide : BeginCodeSnippet
#include "itkGeodesicActiveContourShapePriorLevelSetImageFilter.h"
#include "itkChangeInformationImageFilter.h"
#include "itkBoundedReciprocalImageFilter.h"
// Software Guide : EndCodeSnippet


//  Software Guide : BeginLatex
//
//  Next, we include the headers of the objects involved in shape
//  modeling and estimation.
//
//  Software Guide : EndLatex


// Software Guide : BeginCodeSnippet
#include "itkPCAShapeSignedDistanceFunction.h"
#include "itkEuler2DTransform.h"
#include "itkOnePlusOneEvolutionaryOptimizer.h"
#include "itkNormalVariateGenerator.h"
#include "itkNumericSeriesFileNames.h"
// Software Guide : EndCodeSnippet

#include "itkCurvatureAnisotropicDiffusionImageFilter.h"
#include "itkGradientMagnitudeRecursiveGaussianImageFilter.h"
#include "itkFastMarchingImageFilter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkBinaryThresholdImageFilter.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkSpatialFunctionImageEvaluatorFilter.h"

// Software Guide : BeginLatex
//
// Given the numerous parameters involved in tuning this segmentation method
// it is not uncommon for a segmentation process to
// run for several minutes and still produce an unsatisfactory result. For
// debugging purposes it is quite helpful to track the evolution of the
// segmentation as it progresses. The following defines a
// custom \doxygen{Command} class
// for monitoring the RMS change and shape parameters at each iteration.
//
//  \index{itk::Geodesic\-Active\-Contour\-Shape\-Prior\-LevelSet\-Image\-Filter!Monitoring}
//  \index{itk::Shape\-Prior\-Segmentation\-Level\-Set\-Image\-Filter!Monitoring}
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkCommand.h"

template <class TFilter>
class CommandIterationUpdate : public itk::Command
{
public:
  using Self = CommandIterationUpdate;
  using Superclass = itk::Command;
  using Pointer = itk::SmartPointer<Self>;
  itkNewMacro(Self);

protected:
  CommandIterationUpdate() = default;

public:
  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
  {
    const auto * filter = static_cast<const TFilter *>(object);
    if (typeid(event) != typeid(itk::IterationEvent))
    {
      return;
    }

    std::cout << filter->GetElapsedIterations() << ": ";
    std::cout << filter->GetRMSChange() << " ";
    std::cout << filter->GetCurrentParameters() << std::endl;
  }
};
// Software Guide : EndCodeSnippet


int
main(int argc, char * argv[])
{
  if (argc < 18)
  {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];
    std::cerr << " inputImage  outputImage";
    std::cerr << " seed1X seed1Y";
    std::cerr << " seed2X seed2Y";
    std::cerr << " seed3X seed3Y";
    std::cerr << " initialDistance";
    std::cerr << " sigma";
    std::cerr << " propagationScaling shapePriorScaling";
    std::cerr << " meanShapeImage numberOfModes shapeModeFilePattern";
    std::cerr << " startX startY" << std::endl;
    return EXIT_FAILURE;
  }


  //  Software Guide : BeginLatex
  //
  //  We define the image type using a particular pixel type and
  //  dimension. In this case we will use 2D \code{float} images.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using InternalPixelType = float;
  constexpr unsigned int Dimension = 2;
  using InternalImageType = itk::Image<InternalPixelType, Dimension>;
  // Software Guide : EndCodeSnippet


  //  The following lines instantiate the thresholding filter that will
  //  process the final level set at the output of the
  //  GeodesicActiveContourLevelSetImageFilter.
  //
  using OutputPixelType = unsigned char;
  using OutputImageType = itk::Image<OutputPixelType, Dimension>;
  using ThresholdingFilterType =
    itk::BinaryThresholdImageFilter<InternalImageType, OutputImageType>;

  auto thresholder = ThresholdingFilterType::New();

  thresholder->SetLowerThreshold(-1000.0);
  thresholder->SetUpperThreshold(0.0);

  thresholder->SetOutsideValue(0);
  thresholder->SetInsideValue(255);


  // We instantiate reader and writer types in the following lines.
  //
  using ReaderType = itk::ImageFileReader<InternalImageType>;
  using WriterType = itk::ImageFileWriter<OutputImageType>;

  auto reader = ReaderType::New();
  auto writer = WriterType::New();

  reader->SetFileName(argv[1]);
  writer->SetFileName(argv[2]);


  //  The RescaleIntensityImageFilter type is declared below. This filter will
  //  renormalize image before sending them to writers.
  //
  using CastFilterType =
    itk::RescaleIntensityImageFilter<InternalImageType, OutputImageType>;


  //  The \doxygen{CurvatureAnisotropicDiffusionImageFilter} type is
  //  instantiated using the internal image type.
  //
  using SmoothingFilterType =
    itk::CurvatureAnisotropicDiffusionImageFilter<InternalImageType,
                                                  InternalImageType>;

  auto smoothing = SmoothingFilterType::New();


  //  The types of the
  //  GradientMagnitudeRecursiveGaussianImageFilter is
  //  instantiated using the internal image type.
  //
  using GradientFilterType =
    itk::GradientMagnitudeRecursiveGaussianImageFilter<InternalImageType,
                                                       InternalImageType>;

  auto gradientMagnitude = GradientFilterType::New();


  //  We declare now the type of the FastMarchingImageFilter that
  //  will be used to generate the initial level set in the form of a distance
  //  map.
  //
  using FastMarchingFilterType =
    itk::FastMarchingImageFilter<InternalImageType, InternalImageType>;


  //  Next we construct one filter of this class using the \code{New()}
  //  method.
  //
  auto fastMarching = FastMarchingFilterType::New();

  //  Software Guide : BeginLatex
  //
  //  The following line instantiate a
  //  \doxygen{GeodesicActiveContourShapePriorLevelSetImageFilter}
  //  using the \code{New()} method.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using GeodesicActiveContourFilterType =
    itk::GeodesicActiveContourShapePriorLevelSetImageFilter<
      InternalImageType,
      InternalImageType>;
  auto geodesicActiveContour = GeodesicActiveContourFilterType::New();
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  // The \doxygen{ChangeInformationImageFilter} is the first filter in the
  // preprocessing stage and is used to force the image origin to the center
  // of the image.
  //
  //  \index{itk::ChangeInformationImageFilter!CenterImageOn()}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using CenterFilterType =
    itk::ChangeInformationImageFilter<InternalImageType>;

  auto center = CenterFilterType::New();
  center->CenterImageOn();
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  // In this example, we will use the bounded reciprocal $1/(1+x)$ of
  // the image gradient magnitude as the edge potential feature image.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using ReciprocalFilterType =
    itk::BoundedReciprocalImageFilter<InternalImageType, InternalImageType>;

  auto reciprocal = ReciprocalFilterType::New();
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  In the GeodesicActiveContourShapePriorLevelSetImageFilter, scaling
  //  parameters are used to trade off between the propagation (inflation),
  //  the curvature (smoothing), the advection, and the shape influence terms.
  //  These parameters are set
  //  using methods \code{SetPropagationScaling()},
  //  \code{SetCurvatureScaling()}, \code{SetAdvectionScaling()} and
  //  \code{SetShapePriorScaling()}. In this
  //  example, we will set the curvature and advection scales to one and let
  //  the propagation and shape prior scale be command-line arguments.
  //
  //  \index{itk::Geodesic\-Active\-Contour\-Shape\-Prior\-LevelSet\-Image\-Filter!SetPropagationScaling()}
  //  \index{itk::Shape\-Prior\-Segmentation\-Level\-Set\-Image\-Filter!SetPropagationScaling()}
  //  \index{itk::Geodesic\-Active\-Contour\-Shape\-Prior\-LevelSet\-Image\-Filter!SetCurvatureScaling()}
  //  \index{itk::Shape\-Prior\-Segmentation\-Level\-Set\-Image\-Filter!SetCurvatureScaling()}
  //  \index{itk::Geodesic\-Active\-Contour\-Shape\-Prior\-LevelSet\-Image\-Filter!SetAdvectionScaling()}
  //  \index{itk::Shape\-Prior\-Segmentation\-Level\-Set\-Image\-Filter!SetAdvectionScaling()}
  //
  //  Software Guide : EndLatex

  const double propagationScaling = std::stod(argv[11]);
  const double shapePriorScaling = std::stod(argv[12]);

  //  Software Guide : BeginCodeSnippet
  geodesicActiveContour->SetPropagationScaling(propagationScaling);
  geodesicActiveContour->SetShapePriorScaling(shapePriorScaling);
  geodesicActiveContour->SetCurvatureScaling(1.0);
  geodesicActiveContour->SetAdvectionScaling(1.0);
  //  Software Guide : EndCodeSnippet

  //  Once activated the level set evolution will stop if the convergence
  //  criteria or if the maximum number of iterations is reached.  The
  //  convergence criteria is defined in terms of the root mean squared (RMS)
  //  change in the level set function. The evolution is said to have
  //  converged if the RMS change is below a user specified threshold.  In a
  //  real application is desirable to couple the evolution of the zero set
  //  to a visualization module allowing the user to follow the evolution of
  //  the zero set. With this feedback, the user may decide when to stop the
  //  algorithm before the zero set leaks through the regions of low gradient
  //  in the contour of the anatomical structure to be segmented.

  geodesicActiveContour->SetMaximumRMSError(0.005);
  geodesicActiveContour->SetNumberOfIterations(400);

  //  Software Guide : BeginLatex
  //
  //  Each iteration, the current ``best-fit'' shape is estimated from the
  //  edge potential image and the current contour. To increase speed, only
  //  information within the sparse field layers of the current contour is
  //  used in the estimation. The default number of sparse field layers is the
  //  same as the ImageDimension which does not contain enough information to
  //  get a reliable best-fit shape estimate. Thus, we override the default
  //  and set the number of layers to 4.
  //
  //  Software Guide : EndLatex

  //  Software Guide : BeginCodeSnippet
  geodesicActiveContour->SetNumberOfLayers(4);
  //  Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  The filters are then connected in a pipeline as illustrated in
  //  Figure~\ref{fig:GeodesicActiveContourShapePriorCollaborationDiagram}.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  center->SetInput(reader->GetOutput());
  smoothing->SetInput(center->GetOutput());
  gradientMagnitude->SetInput(smoothing->GetOutput());
  reciprocal->SetInput(gradientMagnitude->GetOutput());

  geodesicActiveContour->SetInput(fastMarching->GetOutput());
  geodesicActiveContour->SetFeatureImage(reciprocal->GetOutput());

  thresholder->SetInput(geodesicActiveContour->GetOutput());
  writer->SetInput(thresholder->GetOutput());
  // Software Guide : EndCodeSnippet


  //  The CurvatureAnisotropicDiffusionImageFilter requires a couple of
  //  parameter to be defined. The following are typical values for $2D$
  //  images. However they may have to be adjusted depending on the amount of
  //  noise present in the input image. This filter has been discussed in
  //  section~\ref{sec:GradientAnisotropicDiffusionImageFilter}.

  smoothing->SetTimeStep(0.125);
  smoothing->SetNumberOfIterations(5);
  smoothing->SetConductanceParameter(9.0);


  //  The GradientMagnitudeRecursiveGaussianImageFilter performs the
  //  equivalent of a convolution with a Gaussian kernel, followed by a
  //  derivative operator. The sigma of this Gaussian can be used to control
  //  the range of influence of the image edges. This filter has been
  //  discussed in
  //  Section~\ref{sec:GradientMagnitudeRecursiveGaussianImageFilter}.

  const double sigma = std::stod(argv[10]);
  gradientMagnitude->SetSigma(sigma);


  //  The FastMarchingImageFilter requires the user to provide a seed
  //  point from which the level set will be generated. The user can actually
  //  pass not only one seed point but a set of them. Note that the
  //  FastMarchingImageFilter is used here only as a helper in the
  //  determination of an initial level set. We could have used the
  //  \doxygen{DanielssonDistanceMapImageFilter} in the same way.
  //
  //  The seeds are passed stored in a container. The type of this
  //  container is defined as \code{NodeContainer} among the
  //  FastMarchingImageFilter traits.
  //
  using NodeContainer = FastMarchingFilterType::NodeContainer;
  using NodeType = FastMarchingFilterType::NodeType;

  auto seeds = NodeContainer::New();

  InternalImageType::IndexType seedPosition;

  seedPosition[0] = std::stoi(argv[3]);
  seedPosition[1] = std::stoi(argv[4]);


  //  Nodes are created as stack variables and initialized with a value and an
  //  \doxygen{Index} position. Note that here we assign the value of minus
  //  the user-provided distance to the unique node of the seeds passed to the
  //  FastMarchingImageFilter. In this way, the value will increment
  //  as the front is propagated, until it reaches the zero value
  //  corresponding to the contour. After this, the front will continue
  //  propagating until it fills up the entire image. The initial distance is
  //  taken here from the command line arguments. The rule of thumb for the
  //  user is to select this value as the distance from the seed points at
  //  which she want the initial contour to be.
  const double initialDistance = std::stod(argv[9]);

  NodeType node;

  const double seedValue = -initialDistance;

  node.SetValue(seedValue);
  node.SetIndex(seedPosition);


  //  The list of nodes is initialized and then every node is inserted using
  //  the \code{InsertElement()}.

  seeds->Initialize();
  seeds->InsertElement(0, node);

  seedPosition[0] = std::stoi(argv[5]);
  seedPosition[1] = std::stoi(argv[6]);
  node.SetIndex(seedPosition);
  seeds->InsertElement(1, node);

  seedPosition[0] = std::stoi(argv[7]);
  seedPosition[1] = std::stoi(argv[8]);
  node.SetIndex(seedPosition);
  seeds->InsertElement(2, node);


  //  The set of seed nodes is passed now to the
  //  FastMarchingImageFilter with the method
  //  \code{SetTrialPoints()}.
  //
  fastMarching->SetTrialPoints(seeds);


  //  Since the FastMarchingImageFilter is used here just as a
  //  Distance Map generator. It does not require a speed image as input.
  //  Instead the constant value $1.0$ is passed using the
  //  \code{SetSpeedConstant()} method.
  //
  fastMarching->SetSpeedConstant(1.0);


  //  Here we configure all the writers required to see the intermediate
  //  outputs of the pipeline. This is added here only for
  //  pedagogical/debugging purposes. These intermediate output are normally
  //  not required. Only the output of the final thresholding filter should be
  //  relevant.  Observing intermediate output is helpful in the process of
  //  fine tuning the parameters of filters in the pipeline.
  //
  auto caster1 = CastFilterType::New();
  auto caster2 = CastFilterType::New();
  auto caster3 = CastFilterType::New();
  auto caster4 = CastFilterType::New();

  auto writer1 = WriterType::New();
  auto writer2 = WriterType::New();
  auto writer3 = WriterType::New();
  auto writer4 = WriterType::New();

  caster1->SetInput(smoothing->GetOutput());
  writer1->SetInput(caster1->GetOutput());
  writer1->SetFileName(
    "GeodesicActiveContourShapePriorImageFilterOutput1.png");
  caster1->SetOutputMinimum(0);
  caster1->SetOutputMaximum(255);
  writer1->Update();

  caster2->SetInput(gradientMagnitude->GetOutput());
  writer2->SetInput(caster2->GetOutput());
  writer2->SetFileName(
    "GeodesicActiveContourShapePriorImageFilterOutput2.png");
  caster2->SetOutputMinimum(0);
  caster2->SetOutputMaximum(255);
  writer2->Update();

  caster3->SetInput(reciprocal->GetOutput());
  writer3->SetInput(caster3->GetOutput());
  writer3->SetFileName(
    "GeodesicActiveContourShapePriorImageFilterOutput3.png");
  caster3->SetOutputMinimum(0);
  caster3->SetOutputMaximum(255);
  writer3->Update();

  caster4->SetInput(fastMarching->GetOutput());
  writer4->SetInput(caster4->GetOutput());
  writer4->SetFileName(
    "GeodesicActiveContourShapePriorImageFilterOutput4.png");
  caster4->SetOutputMinimum(0);
  caster4->SetOutputMaximum(255);


  //  The FastMarchingImageFilter requires the user to specify the
  //  size of the image to be produced as output. This is done using the
  //  \code{SetOutputRegion()}. Note that the size is obtained here from the
  //  output image of the centering filter. The size of this image is valid
  //  only after the \code{Update()} methods of this filter has been called
  //  directly or indirectly.
  //
  fastMarching->SetOutputRegion(center->GetOutput()->GetBufferedRegion());
  fastMarching->SetOutputSpacing(center->GetOutput()->GetSpacing());
  fastMarching->SetOutputOrigin(center->GetOutput()->GetOrigin());


  //  Software Guide : BeginLatex
  //
  //  Next, we define the shape model. In this example,
  //  we use an implicit shape model based on the principal components
  //  such that:
  //
  //  \begin{equation}
  //  \psi^{*}(\mathbf{x}) = \mu(\mathbf{x}) + \sum_k \alpha_k u_k(\mathbf{x})
  //  \end{equation}
  //
  //  where $\mu(\mathbf{x})$ is the mean signed distance computed from
  //  training set of segmented objects and $u_k(\mathbf{x})$ are the first
  //  $K$ principal components of the offset (signed distance - mean). The
  //  coefficients $\{\alpha_k\}$ form the set of \emph{shape} parameters.
  //
  //  Given a set of training data, the \doxygen{ImagePCAShapeModelEstimator}
  //  can be used to obtain
  //  the mean and principal mode shape images required by
  //  PCAShapeSignedDistanceFunction.
  //
  //  \index{itk::PCAShapeSignedDistanceFunction!New()}
  //  \index{itk::PCAShapeSignedDistanceFunction!SetNumberOfPrincipalComponents()}
  //
  //
  //  Software Guide : EndLatex

  const unsigned int numberOfPCAModes = std::stoi(argv[14]);

  // Software Guide : BeginCodeSnippet
  using ShapeFunctionType =
    itk::PCAShapeSignedDistanceFunction<double, Dimension, InternalImageType>;

  auto shape = ShapeFunctionType::New();

  shape->SetNumberOfPrincipalComponents(numberOfPCAModes);
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  In this example, we will read the mean shape and
  //  principal mode images from file. We will assume that
  //  the filenames of the mode images form a numeric series starting from
  //  index 0.
  //
  //  \index{itk::PCAShapeSignedDistanceFunction!SetMeanImage()}
  //  \index{itk::PCAShapeSignedDistanceFunction!SetPrincipalComponentsImages()}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  auto meanShapeReader = ReaderType::New();
  meanShapeReader->SetFileName(argv[13]);
  meanShapeReader->Update();

  std::vector<InternalImageType::Pointer> shapeModeImages(numberOfPCAModes);

  auto fileNamesCreator = itk::NumericSeriesFileNames::New();

  fileNamesCreator->SetStartIndex(0);
  fileNamesCreator->SetEndIndex(numberOfPCAModes - 1);
  fileNamesCreator->SetSeriesFormat(argv[15]);
  const std::vector<std::string> & shapeModeFileNames =
    fileNamesCreator->GetFileNames();

  for (unsigned int k = 0; k < numberOfPCAModes; ++k)
  {
    auto shapeModeReader = ReaderType::New();
    shapeModeReader->SetFileName(shapeModeFileNames[k].c_str());
    shapeModeReader->Update();
    shapeModeImages[k] = shapeModeReader->GetOutput();
  }

  shape->SetMeanImage(meanShapeReader->GetOutput());
  shape->SetPrincipalComponentImages(shapeModeImages);
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Further we assume that the shape modes have been normalized
  // by multiplying with the corresponding singular value. Hence,
  // we can set the principal component standard deviations to all
  // ones.
  //
  //  \index{itk::PCAShapeSignedDistanceFunction!Set\-Principal\-Component\-Standard\-Deviations()}
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  ShapeFunctionType::ParametersType pcaStandardDeviations(numberOfPCAModes);
  pcaStandardDeviations.Fill(1.0);

  shape->SetPrincipalComponentStandardDeviations(pcaStandardDeviations);
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Next, we instantiate a \doxygen{Euler2DTransform} and connect it to the
  // PCASignedDistanceFunction. The transform represent
  // the pose of the shape. The parameters of the transform
  // forms the set of \emph{pose} parameters.
  //
  //  \index{itk::PCAShapeSignedDistanceFunction!SetTransform()}
  //  \index{itk::ShapeSignedDistanceFunction!SetTransform()}
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using TransformType = itk::Euler2DTransform<double>;
  auto transform = TransformType::New();

  shape->SetTransform(transform);
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Before updating the level set at each iteration, the parameters
  // of the current best-fit shape is estimated by minimizing the
  // \doxygen{ShapePriorMAPCostFunction}. The cost function is composed of
  // four terms: contour fit, image fit, shape prior and pose prior.
  // The user can specify the weights applied to each term.
  //
  //  \index{itk::ShapePriorMAPCostFunction!SetWeights()}
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using CostFunctionType =
    itk::ShapePriorMAPCostFunction<InternalImageType, InternalPixelType>;

  auto costFunction = CostFunctionType::New();

  CostFunctionType::WeightsType weights;
  weights[0] = 1.0;  // weight for contour fit term
  weights[1] = 20.0; // weight for image fit term
  weights[2] = 1.0;  // weight for shape prior term
  weights[3] = 1.0;  // weight for pose prior term

  costFunction->SetWeights(weights);
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Contour fit measures the likelihood of seeing the current
  // evolving contour for a given set of shape/pose parameters.
  // This is computed by counting the number of pixels inside
  // the current contour but outside the current shape.
  //
  // Image fit measures the likelihood of seeing certain image
  // features for a given set of shape/pose parameters. This is
  // computed by assuming that ( 1 - edge potential ) approximates
  // a zero-mean, unit variance Gaussian along the normal of
  // the evolving contour. Image fit is then computed by computing
  // the Laplacian goodness of fit of the Gaussian:
  //
  // \begin{equation}
  // \sum \left( G(\psi(\mathbf{x})) - |1 - g(\mathbf{x})| \right)^2
  // \end{equation}
  //
  // where $G$ is a zero-mean, unit variance Gaussian and $g$ is
  // the edge potential feature image.
  //
  // The pose parameters are assumed to have a uniform distribution
  // and hence do not contribute to the cost function.
  // The shape parameters are assumed to have a Gaussian distribution.
  // The parameters of the distribution are user-specified. Since we
  // assumed the principal modes have already been normalized,
  // we set the distribution to zero mean and unit variance.
  //
  //  \index{itk::ShapePriorMAPCostFunction!SetShapeParameterMeans()}
  //  \index{itk::ShapePriorMAPCostFunction!SetShapeParameterStandardDeviations()}
  //
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  CostFunctionType::ArrayType mean(shape->GetNumberOfShapeParameters());
  CostFunctionType::ArrayType stddev(shape->GetNumberOfShapeParameters());

  mean.Fill(0.0);
  stddev.Fill(1.0);
  costFunction->SetShapeParameterMeans(mean);
  costFunction->SetShapeParameterStandardDeviations(stddev);
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // In this example, we will use the
  // \doxygen{OnePlusOneEvolutionaryOptimizer} to optimize the cost function.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using OptimizerType = itk::OnePlusOneEvolutionaryOptimizer;
  auto optimizer = OptimizerType::New();
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // The evolutionary optimization algorithm is based on testing
  // random permutations of the parameters. As such, we need to provide
  // the optimizer with a random number generator. In the following lines,
  // we create a \doxygen{NormalVariateGenerator}, seed it, and
  // connect it to the optimizer.
  //
  //  \index{itk::Statistics::NormalVariateGenerator!Initialize()}
  //  \index{itk::OnePlusOneEvolutionaryOptimizer!SetNormalVariateGenerator()}
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using GeneratorType = itk::Statistics::NormalVariateGenerator;
  auto generator = GeneratorType::New();

  generator->Initialize(20020702);

  optimizer->SetNormalVariateGenerator(generator);
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // The cost function has $K+3$ parameters. The first $K$
  // parameters are the principal component multipliers, followed
  // by the 2D rotation parameter (in radians) and the x- and
  // y- translation parameters (in mm).  We need to carefully
  // scale the different types of parameters to compensate
  // for the differences in the dynamic ranges of the parameters.
  //
  //  \index{itk::OnePlusOneEvolutionaryOptimizer!SetScales()}
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  OptimizerType::ScalesType scales(shape->GetNumberOfParameters());
  scales.Fill(1.0);
  for (unsigned int k = 0; k < numberOfPCAModes; ++k)
  {
    scales[k] = 20.0; // scales for the pca mode multiplier
  }
  scales[numberOfPCAModes] = 350.0; // scale for 2D rotation
  optimizer->SetScales(scales);
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Next, we specify the initial radius, the shrink and
  // grow mutation factors and termination criteria of the optimizer.
  // Since the best-fit shape is re-estimated each iteration of
  // the curve evolution, we do not need to spend too much time finding the
  // true minimizing solution each time; we only need to head towards it. As
  // such, we only require a small number of optimizer iterations.
  //
  //  \index{itk::OnePlusOneEvolutionaryOptimizer!Initialize()}
  //  \index{itk::OnePlusOneEvolutionaryOptimizer!SetEpsilon()}
  //  \index{itk::OnePlusOneEvolutionaryOptimizer!SetMaximumIteration()}
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  double initRadius = 1.05;
  double grow = 1.1;
  double shrink = pow(grow, -0.25);
  optimizer->Initialize(initRadius, grow, shrink);

  optimizer->SetEpsilon(1.0e-6); // minimal search radius

  optimizer->SetMaximumIteration(15);
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Before starting the segmentation process we need to also supply the
  // initial best-fit shape estimate. In this example, we start with the
  // unrotated mean shape with the initial x- and y- translation specified
  // through command-line arguments.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  ShapeFunctionType::ParametersType parameters(
    shape->GetNumberOfParameters());
  parameters.Fill(0.0);
  parameters[numberOfPCAModes + 1] = std::stod(argv[16]); // startX
  parameters[numberOfPCAModes + 2] = std::stod(argv[17]); // startY
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Finally, we connect all the components to the filter and add our
  // observer.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  geodesicActiveContour->SetShapeFunction(shape);
  geodesicActiveContour->SetCostFunction(costFunction);
  geodesicActiveContour->SetOptimizer(optimizer);
  geodesicActiveContour->SetInitialParameters(parameters);

  using CommandType = CommandIterationUpdate<GeodesicActiveContourFilterType>;
  auto observer = CommandType::New();
  geodesicActiveContour->AddObserver(itk::IterationEvent(), observer);
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  The invocation of the \code{Update()} method on the writer triggers the
  //  execution of the pipeline.  As usual, the call is placed in a
  //  \code{try/catch} block to handle exceptions should errors occur.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  try
  {
    writer->Update();
  }
  catch (const itk::ExceptionObject & excep)
  {
    std::cerr << "Exception caught !" << std::endl;
    std::cerr << excep << std::endl;
    return EXIT_FAILURE;
  }
  // Software Guide : EndCodeSnippet

  // Print out some useful information
  std::cout << std::endl;
  std::cout << "Max. no. iterations: "
            << geodesicActiveContour->GetNumberOfIterations() << std::endl;
  std::cout << "Max. RMS error: "
            << geodesicActiveContour->GetMaximumRMSError() << std::endl;
  std::cout << std::endl;
  std::cout << "No. elpased iterations: "
            << geodesicActiveContour->GetElapsedIterations() << std::endl;
  std::cout << "RMS change: " << geodesicActiveContour->GetRMSChange()
            << std::endl;
  std::cout << "Parameters: " << geodesicActiveContour->GetCurrentParameters()
            << std::endl;

  writer4->Update();


  // The following writer type is used to save the output of the time-crossing
  // map in a file with appropriate pixel representation. The advantage of
  // saving this image in native format is that it can be used with a viewer
  // to help determine an appropriate threshold to be used on the output of
  // the fastmarching filter.
  //
  using InternalWriterType = itk::ImageFileWriter<InternalImageType>;

  auto mapWriter = InternalWriterType::New();
  mapWriter->SetInput(fastMarching->GetOutput());
  mapWriter->SetFileName(
    "GeodesicActiveContourShapePriorImageFilterOutput4.mha");
  mapWriter->Update();

  auto speedWriter = InternalWriterType::New();
  speedWriter->SetInput(reciprocal->GetOutput());
  speedWriter->SetFileName(
    "GeodesicActiveContourShapePriorImageFilterOutput3.mha");
  speedWriter->Update();

  auto gradientWriter = InternalWriterType::New();
  gradientWriter->SetInput(gradientMagnitude->GetOutput());
  gradientWriter->SetFileName(
    "GeodesicActiveContourShapePriorImageFilterOutput2.mha");
  gradientWriter->Update();

  // Also write out the initial and final best fit shape
  using EvaluatorFilterType =
    itk::SpatialFunctionImageEvaluatorFilter<ShapeFunctionType,
                                             InternalImageType,
                                             InternalImageType>;

  auto evaluator = EvaluatorFilterType::New();
  evaluator->SetInput(geodesicActiveContour->GetOutput());
  evaluator->SetFunction(shape);
  shape->SetParameters(geodesicActiveContour->GetInitialParameters());

  thresholder->SetInput(evaluator->GetOutput());
  writer->SetFileName(
    "GeodesicActiveContourShapePriorImageFilterOutput5.png");
  writer->Update();

  shape->SetParameters(geodesicActiveContour->GetCurrentParameters());
  evaluator->Modified();
  writer->SetFileName(
    "GeodesicActiveContourShapePriorImageFilterOutput6.png");
  writer->Update();


  //  Software Guide : BeginLatex
  //
  //  Deviating from previous examples, we will demonstrate this example using
  //  \code{BrainMidSagittalSlice.png}
  //  (Figure~\ref{fig:GeodesicActiveContourShapePriorImageFilterOutput},
  //  left) from the \code{Examples/Data} directory. The aim here is to
  //  segment the corpus callosum from the image using a shape model defined
  //  by \code{CorpusCallosumMeanShape.mha} and the first three principal
  //  components \code{CorpusCallosumMode0.mha},
  //  \code{CorpusCallosumMode1.mha} and \code{CorpusCallosumMode12.mha}. As
  //  shown in Figure~\ref{fig:CorpusCallosumPCAModes}, the first mode
  //  captures scaling, the second mode captures the shifting of mass between
  //  the rostrum and the splenium and the third mode captures the degree of
  //  curvature. Segmentation results with and without shape guidance are
  //  shown in
  //  Figure~\ref{fig:GeodesicActiveContourShapePriorImageFilterOutput2}.
  //
  //
  //  \begin{figure} \center
  //  \includegraphics[width=0.30\textwidth]{BrainMidSagittalSlice}
  //  \includegraphics[width=0.30\textwidth]{GeodesicActiveContourShapePriorImageFilterOutput5}
  //  \itkcaption[GeodesicActiveContourShapePriorImageFilter input image and
  //  initial model]{ The input image to the
  //  GeodesicActiveContourShapePriorLevelSetImageFilter is a synthesized
  //  MR-T1 mid-sagittal slice ($217 \times 180$ pixels, $1 \times 1$ mm
  //  spacing) of the brain (left) and the initial best-fit shape (right)
  //  chosen to roughly overlap the corpus callosum in the image to be
  //  segmented.}
  //
  //  \label{fig:GeodesicActiveContourShapePriorImageFilterOutput}
  //  \end{figure}
  //
  //
  //  \begin{figure}
  //  \center
  //  \begin{tabular}{cccc}
  //  & $-3\sigma$ & mean & $+3\sigma$ \\ mode 0: &
  //  \includegraphics[width=0.10\textwidth]{CorpusCallosumModeMinus0} &
  //  \includegraphics[width=0.10\textwidth]{CorpusCallosumMeanShape} &
  //  \includegraphics[width=0.10\textwidth]{CorpusCallosumModePlus0} \\ mode
  //  1: & \includegraphics[width=0.10\textwidth]{CorpusCallosumModeMinus1} &
  //  \includegraphics[width=0.10\textwidth]{CorpusCallosumMeanShape} &
  //  \includegraphics[width=0.10\textwidth]{CorpusCallosumModePlus1} \\ mode
  //  2: & \includegraphics[width=0.10\textwidth]{CorpusCallosumModeMinus2} &
  //  \includegraphics[width=0.10\textwidth]{CorpusCallosumMeanShape} &
  //  \includegraphics[width=0.10\textwidth]{CorpusCallosumModePlus2}
  //  \\ \end{tabular}
  //  \itkcaption[Corpus callosum PCA modes]{First three PCA
  //  modes of a low-resolution
  //  ($58 \times 31$ pixels, $2 \times 2$ mm spacing) corpus callosum model
  //  used in the shape guided geodesic active contours example.}
  //
  //  \label{fig:CorpusCallosumPCAModes}
  //  \end{figure}
  //
  //  A sigma value of $1.0$ was used to compute the image gradient and the
  //  propagation and shape prior scaling are respectively set to $0.5$ and
  //  $0.02$. An initial level set was created by placing one seed point in
  //  the rostrum $(60,102)$, one in the splenium $(120, 85)$ and one
  //  centrally in the body $(88,83)$ of the corpus callosum with
  //  an initial radius of $6$ pixels at each seed position.
  //  The best-fit shape was initially placed with a translation of
  //  $(10,0)$mm so that it roughly overlapped
  //  the corpus callosum in the image as shown in
  //  Figure~\ref{fig:GeodesicActiveContourShapePriorImageFilterOutput}
  //  (right).
  //
  //  From Figure~\ref{fig:GeodesicActiveContourShapePriorImageFilterOutput2}
  //  it can be observed that without shape guidance (left), segmentation
  //  using geodesic active contour leaks in the regions where the corpus
  //  callosum blends into the surrounding brain tissues. With shape guidance
  //  (center), the segmentation is constrained by the global shape model to
  //  prevent leaking.
  //
  //  The final best-fit shape parameters after the segmentation process is:
  //
  //  \begin{verbatim}
  //  Parameters: [-0.384988, -0.578738, 0.557793, 0.275202, 16.9992, 4.73473]
  //  \end{verbatim}
  //
  //  and is shown in
  //  Figure~\ref{fig:GeodesicActiveContourShapePriorImageFilterOutput2}
  //  (right). Note that a $0.28$ radian ($15.8$ degree) rotation has been
  //  introduced to match the model to the corpus callosum in the image.
  //  Additionally, a negative weight for the first mode shrinks the size
  //  relative to the mean shape. A negative weight for the second mode shifts
  //  the mass to splenium, and a positive weight for the third mode increases
  //  the curvature. It can also be observed that the final segmentation is a
  //  combination of the best-fit shape with additional local deformation. The
  //  combination of both global and local shape allows the segmentation to
  //  capture fine details not represented in the shape model.
  //
  //
  //  \begin{figure} \center
  //  \includegraphics[width=0.30\textwidth]{GeodesicActiveContourShapePriorImageFilterOutput1}
  //  \includegraphics[width=0.30\textwidth]{GeodesicActiveContourShapePriorImageFilterOutput2}
  //  \includegraphics[width=0.30\textwidth]{GeodesicActiveContourShapePriorImageFilterOutput6}
  //  \itkcaption[GeodesicActiveContourShapePriorImageFilter
  //  segmentations]{Corpus callosum segmentation using geodesic active
  //  contours without (left) and with (center) shape guidance. The image on
  //  the right represents the best-fit shape at the end of the segmentation
  //  process.}
  //
  //  \label{fig:GeodesicActiveContourShapePriorImageFilterOutput2}
  //  \end{figure}
  //
  //
  //  Software Guide : EndLatex

  return EXIT_SUCCESS;
}
