AbstractMeshWriter.hpp

/*

Copyright (C) University of Oxford, 2005-2009

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/


#ifndef _ABSTRACTMESHWRITER_HPP_
#define _ABSTRACTMESHWRITER_HPP_

#include "AbstractMesh.hpp"
#include <vector>
#include <string>
#include <fstream>
#include <iostream>
#include <sstream>
#include <iomanip>

#include "Exception.hpp"
#include "OutputFileHandler.hpp"
#include "AbstractMeshReader.hpp"
#include "NodeMap.hpp"


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractMeshWriter
{
protected:
    OutputFileHandler *mpOutputFileHandler; 
    std::string mBaseName; 
    std::vector< std::vector<double> > mNodeData; 
    std::vector< std::vector<unsigned> > mElementData; 
    std::vector< std::vector<unsigned> > mBoundaryFaceData; 
    std::vector< std::vector<double> >::iterator mpNodeIterator; 
    std::vector< std::vector<unsigned> >::iterator mpElementIterator; 
    std::vector< std::vector<unsigned> >::iterator mpBoundaryFaceIterator; 
    bool mIndexFromZero; 
    bool mWriteMetaFile;
public:
    AbstractMeshWriter(const std::string &rDirectory,
                       const std::string &rBaseName,
                       const bool clearOutputDir=true)
            : mBaseName(rBaseName)
    {
        mpOutputFileHandler = new OutputFileHandler(rDirectory, clearOutputDir);
    }
    virtual ~AbstractMeshWriter()
    {
        delete mpOutputFileHandler;
    }
    std::string GetOutputDirectory(void);

    void SetNextNode(std::vector<double> nextNode);
    virtual void SetNextElement(std::vector<unsigned> nextElement);
    void SetNextBoundaryFace(std::vector<unsigned> nextFace);
    void SetNextBoundaryEdge(std::vector<unsigned> nextEdge);
    virtual void WriteFiles()=0;
    unsigned GetNumNodes()
    {
        return mNodeData.size();
    }
    unsigned GetNumElements()
    {
        return mElementData.size();
    }
    unsigned GetNumBoundaryFaces()
    {
        return mBoundaryFaceData.size();
    }
    unsigned GetNumBoundaryEdges()
    {
        return mBoundaryFaceData.size();
    }
    void WriteFilesUsingMesh(AbstractMesh<ELEMENT_DIM, SPACE_DIM>& rMesh);
    void WriteFilesUsingMeshReader(AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader);
    void WriteFilesUsingMeshReader(AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader,
                                   std::vector<unsigned>& rNodePermutation);
};




template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::string AbstractMeshWriter<ELEMENT_DIM, SPACE_DIM>::GetOutputDirectory(void)
{
    return mpOutputFileHandler->GetOutputDirectoryFullPath();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMeshWriter<ELEMENT_DIM, SPACE_DIM>::SetNextNode(std::vector<double> nextNode)
{
    assert (nextNode.size() == SPACE_DIM);
    mNodeData.push_back(nextNode);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMeshWriter<ELEMENT_DIM, SPACE_DIM>::SetNextElement(std::vector<unsigned> nextElement)
{
    assert (nextElement.size() == ELEMENT_DIM+1);
    mElementData.push_back(nextElement);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMeshWriter<ELEMENT_DIM, SPACE_DIM>::SetNextBoundaryFace(std::vector<unsigned> nextFace)
{
    assert (nextFace.size() == ELEMENT_DIM);
    mBoundaryFaceData.push_back(nextFace);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMeshWriter<ELEMENT_DIM, SPACE_DIM>::SetNextBoundaryEdge(std::vector<unsigned> nextEdge)
{
    SetNextBoundaryFace(nextEdge);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteFilesUsingMesh(
     AbstractMesh<ELEMENT_DIM,SPACE_DIM>& rMesh)
{
    NodeMap node_map(rMesh.GetNumAllNodes());
    unsigned new_index=0;
    for (unsigned i=0; i<(unsigned)rMesh.GetNumAllNodes();i++)
    {
        Node<SPACE_DIM>* p_node = rMesh.GetNode(i);

        if (p_node->IsDeleted() == false)
        {
            std::vector<double> coords(SPACE_DIM);
            for (unsigned j=0; j<SPACE_DIM; j++)
            {
                coords[j] = p_node->GetPoint()[j];
            }
            SetNextNode(coords);
            node_map.SetNewIndex(i,new_index++);
        }
        else
        {
            node_map.SetDeleted(i);
        }
    }
    assert(new_index==(unsigned)rMesh.GetNumNodes());

    // Get an iterator over the elements of the mesh
    typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator iter =
        rMesh.GetElementIteratorBegin();

    while (iter != rMesh.GetElementIteratorEnd())
    {
        if ((*iter)->IsDeleted() == false)
        {
            std::vector<unsigned> indices((*iter)->GetNumNodes());
            for (unsigned j=0; j<indices.size(); j++)
            {
                unsigned old_index=(*iter)->GetNodeGlobalIndex(j);
                indices[j] = node_map.GetNewIndex(old_index);
            }
            this->SetNextElement(indices);
        }

        iter++;
    }

    // Get a iterator over the boundary elements of the mesh
    typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::BoundaryElementIterator boundary_iter =
        rMesh.GetBoundaryElementIteratorBegin();
    while (boundary_iter != rMesh.GetBoundaryElementIteratorEnd())
    {
        if ((*boundary_iter)->IsDeleted() == false)
        {
            std::vector<unsigned> indices(ELEMENT_DIM);
            for (unsigned j=0; j<ELEMENT_DIM; j++)
            {
                unsigned old_index=(*boundary_iter)->GetNodeGlobalIndex(j);
                indices[j] = node_map.GetNewIndex(old_index);
            }
            SetNextBoundaryFace(indices);
        }
        boundary_iter++;
    }
    WriteFiles();
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteFilesUsingMeshReader(
    AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader)
{
    for (unsigned i=0; i<rMeshReader.GetNumNodes();i++)
    {
        SetNextNode(rMeshReader.GetNextNode());
    }
    for (unsigned i=0; i<rMeshReader.GetNumElements();i++)
    {
        this->SetNextElement(rMeshReader.GetNextElementData().NodeIndices);
    }
    for (unsigned i=0; i<rMeshReader.GetNumFaces();i++)
    {
        this->SetNextBoundaryFace(rMeshReader.GetNextFaceData().NodeIndices);
    }
    WriteFiles();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteFilesUsingMeshReader(
    AbstractMeshReader<ELEMENT_DIM, SPACE_DIM>& rMeshReader,
    std::vector<unsigned>& rNodePermutation)
{
    if (rNodePermutation.size() == 0)
    {
       WriteFilesUsingMeshReader(rMeshReader);
    }
    else
    {
        mNodeData.resize(rMeshReader.GetNumNodes());        
        for (unsigned i=0; i<rMeshReader.GetNumNodes();i++)
        {
            assert(rNodePermutation[i] < rMeshReader.GetNumNodes());
            mNodeData[ rNodePermutation[i] ] = rMeshReader.GetNextNode();
        }

        for (unsigned i=0; i<rMeshReader.GetNumElements();i++)
        {
            ElementData element = rMeshReader.GetNextElementData();
            
            for(unsigned local_index=0; local_index<element.NodeIndices.size(); local_index++)
            {
                unsigned old_index = element.NodeIndices[local_index];
                element.NodeIndices[local_index] = rNodePermutation[old_index];
            }
            
            SetNextElement(element.NodeIndices);
        }
        
        for (unsigned i=0; i<rMeshReader.GetNumFaces();i++)
        {
            ElementData face = rMeshReader.GetNextFaceData();
            
            for(unsigned local_index=0; local_index<face.NodeIndices.size(); local_index++)
            {
                unsigned old_index = face.NodeIndices[local_index];
                face.NodeIndices[local_index] = rNodePermutation[old_index];
            }
            
            SetNextBoundaryFace(face.NodeIndices);
        }
        WriteFiles();
    }
}

#endif //_ABSTRACTMESHWRITER_HPP_

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