/*=========================================================================
 *
 *  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 section illustrates the full power of
//  \href{http://www.boost.org/more/generic_programming.html}{Generic
//  Programming}.  This is sometimes perceived as \emph{too much of a good
//  thing}!
//
//  The toolkit has been designed to offer flexibility while keeping the
//  complexity of the code to a moderate level. This is achieved in the Mesh
//  by hiding most of its parameters and defining reasonable defaults for
//  them.
//
//  The generic concept of a mesh integrates many different elements. It is
//  possible in principle to use independent types for every one of such
//  elements. The mechanism used in generic programming for specifying the
//  many different types involved in a concept is called \emph{traits}. They
//  are basically the list of all types that interact with the current class.
//
//  The \doxygen{Mesh} is templated over three parameters. So far only two of
//  them have been discussed, namely the \code{PixelType} and the
//  \code{Dimension}. The third parameter is a class providing the set of
//  traits required by the mesh. When the third parameter is omitted a default
//  class is used. This default class is the
//  \doxygen{DefaultStaticMeshTraits}. If you want to customize the types used
//  by the mesh, the way to proceed is to modify the default traits and
//  provide them as the third parameter of the Mesh class instantiation.
//
//  There are two ways of achieving this. The first is to use the existing
//  \doxygen{DefaultStaticMeshTraits} class. This class is itself templated
//  over six parameters.  Customizing those parameters could provide enough
//  flexibility to define a very specific kind of mesh. The second way is to
//  write a traits class from scratch, in which case the easiest way to
//  proceed is to copy the \code{DefaultStaticMeshTraits} into another file
//  and edit its content. Only the first approach is illustrated here. The
//  second is discouraged unless you are familiar with Generic Programming,
//  feel comfortable with C++ templates, and have access to an abundant supply
//  of (Columbian) coffee.
//
//  The first step in customizing the mesh is to include the header file of
//  the Mesh and its static traits.
//
//  \index{itk::DefaultStaticMeshTraits!Header}
//
//  Software Guide : EndLatex


// Software Guide : BeginCodeSnippet
#include "itkMesh.h"
#include "itkDefaultStaticMeshTraits.h"
// Software Guide : EndCodeSnippet

#include "itkLineCell.h"
#include "itkVector.h"
#include "itkMatrix.h"

int
main(int, char *[])
{
  //  Software Guide : BeginLatex
  //
  //  Then the MeshTraits class is instantiated by selecting the types of each
  //  one of its six template arguments. They are in order
  //
  //  \begin{description}
  //  \item[PixelType.] The value type associated with every point.
  //  \item[PointDimension.] The dimension of the space in which the mesh is
  //  embedded. \item[MaxTopologicalDimension.] The highest dimension of the
  //  mesh cells. \item[CoordRepType.] The type used to represent spacial
  //  coordinates. \item[InterpolationWeightType.]  The type used to represent
  //  interpolation weights. \item[CellPixelType.] The value type associated
  //  with every cell. \end{description}
  //
  //  Let's define types and values for each one of those elements. For
  //  example, the following code uses points in 3D space as nodes of the
  //  Mesh. The maximum dimension of the cells will be two, meaning
  //  that this is a 2D manifold better know as a \emph{surface}. The data
  //  type associated with points is defined to be a four-dimensional vector.
  //  This type could represent values of membership for a four-class
  //  segmentation method.  The value selected for the cells are $4\times3$
  //  matrices, which could have for example the derivative of the membership
  //  values with respect to coordinates in space. Finally, a \code{double}
  //  type is selected for representing space coordinates on the mesh points
  //  and also for the weight used for interpolating values.
  //
  //  \index{itk::DefaultStaticMeshTraits!Instantiation}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  constexpr unsigned int PointDimension = 3;
  constexpr unsigned int MaxTopologicalDimension = 2;

  using PixelType = itk::Vector<double, 4>;
  using CellDataType = itk::Matrix<double, 4, 3>;

  using CoordinateType = double;
  using InterpolationWeightType = double;

  using MeshTraits = itk::DefaultStaticMeshTraits<PixelType,
                                                  PointDimension,
                                                  MaxTopologicalDimension,
                                                  CoordinateType,
                                                  InterpolationWeightType,
                                                  CellDataType>;

  using MeshType = itk::Mesh<PixelType, PointDimension, MeshTraits>;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  The \doxygen{LineCell} type can now be instantiated using the traits
  //  taken from the Mesh.
  //
  //  \index{itk::LineCell!Instantiation}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using CellType = MeshType::CellType;
  using LineType = itk::LineCell<CellType>;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Let's now create an Mesh and insert some points on it. Note
  //  that the dimension of the points matches the dimension of the Mesh. Here
  //  we insert a sequence of points that look like a plot of the $log()$
  //  function.
  //
  //  \index{itk::Mesh!New()}
  //  \index{itk::Mesh!SetPoint()}
  //  \index{itk::Mesh!PointType}
  //  \index{itk::Mesh!Pointer}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  MeshType::Pointer mesh = MeshType::New();

  using PointType = MeshType::PointType;
  PointType point;

  constexpr unsigned int numberOfPoints = 10;
  for (unsigned int id = 0; id < numberOfPoints; id++)
  {
    point[0] = 1.565; // Initialize points here
    point[1] = 3.647; // with arbitrary values
    point[2] = 4.129;
    mesh->SetPoint(id, point);
  }
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  A set of line cells is created and associated with the existing points
  //  by using point identifiers. In this simple case, the point identifiers
  //  can be deduced from cell identifiers since the line cells are ordered in
  //  the same way. Note that in the code above, the values assigned to point
  //  components are arbitrary. In a more realistic example, those values
  //  would be computed from another source.
  //
  //  \index{itk::AutoPointer!TakeOwnership()}
  //  \index{CellAutoPointer!TakeOwnership()}
  //  \index{CellType!creation}
  //  \index{itk::Mesh!SetCell()}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  CellType::CellAutoPointer line;
  const unsigned int        numberOfCells = numberOfPoints - 1;
  for (unsigned int cellId = 0; cellId < numberOfCells; cellId++)
  {
    line.TakeOwnership(new LineType);
    line->SetPointId(0, cellId);     // first point
    line->SetPointId(1, cellId + 1); // second point
    mesh->SetCell(cellId, line);     // insert the cell
  }
  // Software Guide : EndCodeSnippet


  std::cout << "Points = " << mesh->GetNumberOfPoints() << std::endl;
  std::cout << "Cells  = " << mesh->GetNumberOfCells() << std::endl;

  //  Software Guide : BeginLatex
  //
  //  Data associated with cells is inserted in the Mesh by using the
  //  \code{SetCellData()} method.  It requires the user to provide an
  //  identifier and the value to be inserted. The identifier should match one
  //  of the inserted cells. In this example, we simply store a
  //  \code{CellDataType} dummy variable named \code{value}.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  for (unsigned int cellId = 0; cellId < numberOfCells; cellId++)
  {
    CellDataType value;
    mesh->SetCellData(cellId, value);
  }

  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Cell data can be read from the Mesh with the
  //  \code{GetCellData()} method. It requires the user to provide the
  //  identifier of the cell for which the data is to be retrieved. The user
  //  should provide also a valid pointer to a location where the data can be
  //  copied.
  //
  //  \index{itk::Mesh!GetCellData()}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  for (unsigned int cellId = 0; cellId < numberOfCells; ++cellId)
  {
    CellDataType value;
    mesh->GetCellData(cellId, &value);
    std::cout << "Cell " << cellId << " = " << value << std::endl;
  }
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Neither \code{SetCellData()} or \code{GetCellData()} are efficient ways
  //  to access cell data. Efficient access to cell data can be achieved
  //  by using the \code{Iterator}s built into the \code{CellDataContainer}.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using CellDataIterator = MeshType::CellDataContainer::ConstIterator;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Note that the \code{ConstIterator} is used here because the data is only
  //  going to be read.  This approach is identical to that already
  //  illustrated for accessing point data. The iterator to the first cell
  //  data item can be obtained with the \code{Begin()} method of the
  //  \code{CellDataContainer}. The past-end iterator is returned by the
  //  \code{End()} method. The cell data container itself can be obtained from
  //  the mesh with the method \code{GetCellData()}.
  //
  //  \index{itk::Mesh!Iterating cell data}
  //  \index{itk::Mesh!GetCellData()}
  //  \index{CellDataContainer!Begin()}
  //  \index{CellDataContainer!End()}
  //  \index{CellDataContainer!Iterator}
  //  \index{CellDataContainer!ConstIterator}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  CellDataIterator cellDataIterator = mesh->GetCellData()->Begin();
  CellDataIterator end = mesh->GetCellData()->End();
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Finally a standard loop is used to iterate over all the cell data
  //  entries. Note the use of the \code{Value()} method used to get the
  //  actual value of the data entry. \code{PixelType} elements are returned
  //  by copy.
  //
  //  \index{CellDataIterator!Value()}
  //  \index{CellDataIterator!increment}
  //
  //  Software Guide : EndLatex


  // Software Guide : BeginCodeSnippet
  while (cellDataIterator != end)
  {
    CellDataType cellValue = cellDataIterator.Value();
    std::cout << cellValue << std::endl;
    ++cellDataIterator;
  }
  // Software Guide : EndCodeSnippet

  return EXIT_SUCCESS;
}