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 *  Copyright Insight Software Consortium
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 *  you may not use this file except in compliance with the License.
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 *         http://www.apache.org/licenses/LICENSE-2.0.txt
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 *  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.
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 *=========================================================================*/

//  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
  const unsigned int PointDimension = 3;
  const unsigned int MaxTopologicalDimension = 2;

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

  typedef double CoordinateType;
  typedef double InterpolationWeightType;

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

  typedef itk::Mesh< PixelType, PointDimension, MeshTraits > MeshType;
  // 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
  typedef MeshType::CellType                CellType;
  typedef itk::LineCell< CellType >         LineType;
  // 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();

  typedef MeshType::PointType PointType;
  PointType point;

  const 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
  typedef MeshType::CellDataContainer::ConstIterator CellDataIterator;
  // 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;
}