VtkMeshWriter.hpp

/*

Copyright (c) 2005-2017, University of Oxford.
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This file is part of Chaste.

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modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
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   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/

#ifndef VTKMESHWRITER_HPP_
#define VTKMESHWRITER_HPP_

#ifdef CHASTE_VTK
//Requires  "sudo aptitude install libvtk5-dev" or similar
#define _BACKWARD_BACKWARD_WARNING_H 1 //Cut out the strstream deprecated warning for now (gcc4.3)
#include <vtkDoubleArray.h>
#include <vtkCellData.h>
#include <vtkPointData.h>
#include <vtkTetra.h>
#include <vtkTriangle.h>
#include <vtkLine.h>
#include <vtkUnstructuredGrid.h>
#include <vtkUnstructuredGridWriter.h>
#include <vtkXMLUnstructuredGridWriter.h>
#include <vtkXMLPUnstructuredGridWriter.h>

#include <vtkDataCompressor.h>
#include "AbstractTetrahedralMeshWriter.hpp"
#include "Version.hpp"


#include <map>

// Forward declaration prevents circular include chain
template<unsigned SPACE_DIM>
class NodesOnlyMesh;

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class VtkMeshWriter : public AbstractTetrahedralMeshWriter<ELEMENT_DIM, SPACE_DIM>
{

//Requires  "sudo aptitude install libvtk5-dev" or similar

private:
    bool mWriteParallelFiles; 
    std::map<unsigned, unsigned> mGlobalToNodeIndexMap; 
    std::vector<std::vector<unsigned> > mNodesToSendPerProcess; 
    std::vector<std::vector<unsigned> > mNodesToReceivePerProcess;  
    NodesOnlyMesh<SPACE_DIM>* mpNodesOnlyMesh;

    vtkUnstructuredGrid* mpVtkUnstructedMesh;

    void MakeVtkMesh();

    void AugmentCellData();

public:

    VtkMeshWriter(const std::string& rDirectory, const std::string& rBaseName, const bool& rCleanDirectory=true);

    void WriteFiles();


     void AddCellData(std::string name, std::vector<double> data);

    void AddCellData(std::string name, std::vector<c_vector<double, SPACE_DIM> > data);

    void AddTensorCellData(std::string name, std::vector<c_vector<double,SPACE_DIM*(SPACE_DIM+1)/2> > data);

    void AddTensorCellData(std::string name, std::vector<c_matrix<double,SPACE_DIM,SPACE_DIM> > data);


    void AddPointData(std::string name, std::vector<double> data);

    void AddPointData(std::string name, std::vector<c_vector<double, SPACE_DIM> > data);

    void AddTensorPointData(std::string name, std::vector<c_matrix<double,SPACE_DIM,SPACE_DIM> > data);

     void SetParallelFiles(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>& rMesh);

    void WriteFilesUsingMesh(AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>& rMesh,
                                     bool keepOriginalElementIndexing=true);

    void AddProvenance(std::string fileName);

    virtual ~VtkMeshWriter();
};

#endif //CHASTE_VTK

#endif /*VTKMESHWRITER_HPP_*/