/*=========================================================================
 *
 *  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
//
//  A \doxygen{Mesh} can contain a variety of cell types. Typical cells are
//  the \doxygen{LineCell}, \doxygen{TriangleCell},
//  \doxygen{QuadrilateralCell}, \doxygen{TetrahedronCell}, and
//  \doxygen{PolygonCell}. Additional flexibility is provided for managing
//  cells at the price of a bit more of complexity than in the case of point
//  management.
//
//  The following code creates a polygonal line in order to illustrate the
//  simplest case of cell management in a mesh. The only cell type used here
//  is the \code{LineCell}. The header file of this class must be included.
//
//  \index{itk::LineCell!Header}
//
//  Software Guide : EndLatex


#include "itkMesh.h"

// Software Guide : BeginCodeSnippet
#include "itkLineCell.h"
// Software Guide : EndCodeSnippet


int
main(int, char *[])
{
  using PixelType = float;
  using MeshType = itk::Mesh<PixelType, 3>;

  //  Software Guide : BeginLatex
  //
  //  For consistency with \code{Mesh}, cell types have to be configured
  //  with a number of custom types taken from the mesh traits. The set of
  //  traits relevant to cells are packaged by the Mesh class into the
  //  \code{CellType} trait. This trait needs to be passed to the actual cell
  //  types at the moment of their instantiation. The following line shows how
  //  to extract the Cell traits from the Mesh type.
  //
  //  \index{itk::Mesh!CellType}
  //  \index{itk::Mesh!traits}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using CellType = MeshType::CellType;
  // Software Guide : EndCodeSnippet


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

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


  //  Software Guide : BeginLatex
  //
  //  The main difference in the way cells and points are managed by
  //  the Mesh is that points are stored by copy on the
  //  \code{PointsContainer} while cells are stored as pointers in the
  //  \code{CellsContainer}.  The reason for using pointers is that cells
  //  use C++ polymorphism on the mesh. This means that the mesh is only
  //  aware of having pointers to a generic cell which is the base
  //  class of all the specific cell types. This architecture makes it
  //  possible to combine different cell types in the same
  //  mesh. Points, on the other hand, are of a single type and have a
  //  small memory footprint, which makes it efficient to copy them
  //  directly into the container.
  //
  //  \index{itk::Cell!CellAutoPointer}
  //  \index{itk::Mesh!CellAutoPointer}
  //  \index{CellAutoPointer}
  //  \index{itk::AutoPointer}
  //
  //  Managing cells by pointers adds another level of complexity to the Mesh
  //  since it is now necessary to establish a protocol to make clear who is
  //  responsible for allocating and releasing the cells' memory. This
  //  protocol is implemented in the form of a specific type of pointer called
  //  the \code{CellAutoPointer}. This pointer, based on the
  //  \doxygen{AutoPointer}, differs in many respects from the
  //  \code{SmartPointer}. The \code{CellAutoPointer} has an internal pointer
  //  to the actual object and a boolean flag that indicates whether the
  //  \code{CellAutoPointer} is responsible for releasing the cell memory when
  //  the time comes for its own destruction. It is said that a
  //  \code{CellAutoPointer} \emph{owns} the cell when it is responsible for
  //  its destruction. At any given time many \code{CellAutoPointer}s can
  //  point to the same cell, but only \textbf{one} \code{CellAutoPointer} can
  //  own the cell.
  //
  //  The \code{CellAutoPointer} trait is defined in the \code{MeshType} and
  //  can be extracted as follows.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using CellAutoPointer = CellType::CellAutoPointer;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Note that the \code{CellAutoPointer} points to a generic cell type. It
  //  is not aware of the actual type of the cell, which could be (for
  //  example) a \code{LineCell}, \code{TriangleCell} or
  //  \code{TetrahedronCell}. This fact will influence the way in which we
  //  access cells later on.
  //
  //  At this point we can actually create a mesh and insert some points on
  //  it.
  //
  //  \index{itk::Mesh!New()}
  //  \index{itk::Mesh!SetPoint()}
  //  \index{itk::Mesh!PointType}
  //
  //  Software Guide : EndLatex

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

  MeshType::PointType p0;
  MeshType::PointType p1;
  MeshType::PointType p2;

  p0[0] = -1.0;
  p0[1] = 0.0;
  p0[2] = 0.0;
  p1[0] = 1.0;
  p1[1] = 0.0;
  p1[2] = 0.0;
  p2[0] = 1.0;
  p2[1] = 1.0;
  p2[2] = 0.0;

  mesh->SetPoint(0, p0);
  mesh->SetPoint(1, p1);
  mesh->SetPoint(2, p2);
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  The following code creates two \code{CellAutoPointers} and initializes
  //  them with newly created cell objects. The actual cell type
  //  created in this case is \code{LineType}. Note that cells are
  //  created with the normal \code{new} C++ operator. The
  //  CellAutoPointer takes ownership of the received pointer by using
  //  the method \code{TakeOwnership()}. Even though this may seem
  //  verbose, it is necessary in order to make it explicit
  //  that the responsibility of memory release is assumed by the
  //  \code{AutoPointer}.
  //
  //  \index{itk::AutoPointer!TakeOwnership()}
  //  \index{CellAutoPointer!TakeOwnership()}
  //  \index{CellType!creation}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  CellAutoPointer line0;
  CellAutoPointer line1;

  line0.TakeOwnership(new LineType);
  line1.TakeOwnership(new LineType);
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  The LineCells should now be associated with points in the mesh. This is
  //  done using the identifiers assigned to points when they were inserted
  //  in the mesh. Every cell type has a specific number of points that must
  //  be associated with it.\footnote{Some cell types like polygons have a
  //  variable number of points associated with them.} For example, a
  //  \code{LineCell} requires two points, a \code{TriangleCell}
  //  requires three, and a \code{TetrahedronCell} requires four. Cells use
  //  an internal numbering system for points. It is simply an index in the
  //  range $\{0,NumberOfPoints-1\}$. The association of points and cells is
  //  done by the \code{SetPointId()} method, which requires the user to
  //  provide the internal index of the point in the cell and the
  //  corresponding \code{PointIdentifier} in the \code{Mesh}. The internal
  //  cell index is the first parameter of \code{SetPointId()} while the mesh
  //  point-identifier is the second.
  //
  //  Software Guide : EndLatex


  // Software Guide : BeginCodeSnippet
  line0->SetPointId(0, 0); // line between points 0 and 1
  line0->SetPointId(1, 1);

  line1->SetPointId(0, 1); // line between points 1 and 2
  line1->SetPointId(1, 2);
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Cells are inserted in the mesh using the \code{SetCell()} method. It
  //  requires an identifier and the AutoPointer to the cell. The Mesh will
  //  take ownership of the cell to which the \code{CellAutoPointer} is
  //  pointing. This is done internally by the \code{SetCell()} method. In
  //  this way, the destruction of the \code{CellAutoPointer} will not
  //  induce the destruction of the associated cell.
  //
  //  \index{itk::Mesh!SetCell()}
  //  \index{SetCell()!itk::Mesh}
  //  \index{itk::Mesh!Inserting cells}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  mesh->SetCell(0, line0);
  mesh->SetCell(1, line1);
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  After serving as an argument of the \code{SetCell()} method, a
  //  \code{CellAutoPointer} no longer holds ownership of the cell. It is
  //  important not to use this same \code{CellAutoPointer} again as
  //  argument to \code{SetCell()} without first securing ownership of
  //  another cell.
  //
  //  Software Guide : EndLatex

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

  //  Software Guide : BeginLatex
  //
  //  The number of Cells currently inserted in the mesh can be queried with
  //  the \code{GetNumberOfCells()} method.
  //
  //  \index{itk::Mesh!GetNumberOfCells()}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  std::cout << "Cells  = " << mesh->GetNumberOfCells() << std::endl;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  In a way analogous to points, cells can be accessed using Iterators to
  //  the \code{CellsContainer} in the mesh. The trait for the cell iterator
  //  can be extracted from the mesh and used to define a local type.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using CellIterator = MeshType::CellsContainer::Iterator;
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Then the iterators to the first and past-end cell in the mesh can be
  //  obtained respectively with the \code{Begin()} and \code{End()}
  //  methods of the \code{CellsContainer}. The \code{CellsContainer} of
  //  the mesh is returned by the \code{GetCells()} method.
  //
  //  \index{itk::Mesh!Iterating cells}
  //  \index{itk::Mesh!GetCells()}
  //  \index{CellsContainer!Begin()}
  //  \index{CellsContainer!End()}
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  CellIterator cellIterator = mesh->GetCells()->Begin();
  CellIterator end = mesh->GetCells()->End();
  // Software Guide : EndCodeSnippet


  //  Software Guide : BeginLatex
  //
  //  Finally, a standard loop is used to iterate over all the cells. Note the
  //  use of the \code{Value()} method used to get the actual pointer to the
  //  cell from the CellIterator. Note also that the value returned is
  //  a pointer to the generic CellType. This pointer must be downcast
  //  in order to be used as actual LineCell types. Safe down-casting is
  //  performed with the \code{dynamic\_cast} operator, which will throw an
  //  exception if the conversion cannot be safely performed.
  //
  //  \index{down casting}
  //  \index{CellIterator!Value()}
  //  \index{CellIterator!increment}
  //  \index{itk::Mesh!CellType casting}
  //  \index{Print()}
  //  \index{CellType!Print()}
  //  \index{CellType!GetNumberOfPoints()}
  //  \index{LineCell!Print()}
  //  \index{LineCell!GetNumberOfPoints()}
  //
  //  Software Guide : EndLatex


  // Software Guide : BeginCodeSnippet
  while (cellIterator != end)
  {
    MeshType::CellType * cellptr = cellIterator.Value();
    auto *               line = dynamic_cast<LineType *>(cellptr);
    if (line == nullptr)
    {
      continue;
    }
    std::cout << line->GetNumberOfPoints() << std::endl;
    ++cellIterator;
  }
  // Software Guide : EndCodeSnippet

  return EXIT_SUCCESS;
}