TrianglesMeshReader.hpp

/*

Copyright (C) University of Oxford, 2005-2011

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 _TRIANGLESMESHREADER_HPP_
#define _TRIANGLESMESHREADER_HPP_

#include <vector>
#include <string>
#include <fstream>
#include "AbstractMeshReader.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class TrianglesMeshReader : public AbstractMeshReader<ELEMENT_DIM,SPACE_DIM>
{

    friend class TestTrianglesMeshReader;//for testing

private:

    bool mIndexFromZero;            
    std::string mFilesBaseName;     
    std::ifstream mNodesFile;       
    std::ifstream mElementsFile;    
    std::ifstream mFacesFile;       
    std::ifstream mNclFile;         
    std::ifstream mCableElementsFile; 
    std::streampos mNodeFileDataStart; 
    std::streamoff mNodeItemWidth;  
    std::streampos mElementFileDataStart; 
    std::streamoff mElementItemWidth;  
    std::streampos mFaceFileDataStart; 
    std::streamoff mFaceItemWidth;  
    std::streampos mNclFileDataStart; 
    std::streamoff mNclItemWidth;  
    unsigned mNumNodes;             
    unsigned mNumElements;          
    unsigned mNumFaces;             
    unsigned mNumCableElements;     
    unsigned mNodesRead;            
    unsigned mElementsRead;         
    unsigned mCableElementsRead;    
    unsigned mFacesRead;            
    unsigned mBoundaryFacesRead;    
    std::vector<unsigned> mOneDimBoundary; 
    unsigned mNumNodeAttributes;    
    std::vector<double> mNodeAttributes; 
    unsigned mMaxNodeBdyMarker;     
    unsigned mNumElementNodes;      
    unsigned mNumElementAttributes; 
    unsigned mNumFaceAttributes;    
    unsigned mNumCableElementAttributes; 
    unsigned mOrderOfElements;      
    unsigned mOrderOfBoundaryElements; 
    unsigned mNodesPerElement;      
    unsigned mNodesPerBoundaryElement; 
    unsigned mMaxContainingElements; 
    bool mEofException; 
    bool mReadContainingElementOfBoundaryElement; 
    bool mFilesAreBinary; 
    bool mMeshIsHexahedral; 
    bool mNclFileAvailable; 
    char* mNodeFileReadBuffer; 
    char* mElementFileReadBuffer; 
    char* mFaceFileReadBuffer; 
    bool mNodePermutationDefined; 
    std::vector<unsigned> mPermutationVector; 
    std::vector<unsigned> mInversePermutationVector; 
//    /** The containing element for each boundary element (obtaining by doing tetgen with the -nn flag).
//     *  In a std::vector rather than the struct to save space if not read.
//     */
//    std::vector<unsigned> mContainingElementsOfBoundaryElement;
//
//    unsigned mIndexIntoContainingElementsVector; /**< Which index to use when GetNextContainingElementOfBoundaryElement() is called */

public:

    TrianglesMeshReader(std::string pathBaseName,
                        unsigned orderOfElements=1,
                        unsigned orderOfBoundaryElements=1,
                        bool readContainingElementsForBoundaryElements=false);

     ~TrianglesMeshReader();

    unsigned GetNumElements() const;

    unsigned GetNumNodes() const;

    unsigned GetNumFaces() const;

    unsigned GetNumCableElements() const;

    unsigned GetNumElementAttributes() const;

    unsigned GetNumFaceAttributes() const;

    unsigned GetNumCableElementAttributes() const;

    void Reset();

    std::vector<double> GetNextNode();

    ElementData GetNextElementData();

    ElementData GetNextFaceData();

    ElementData GetNextCableElementData();


    unsigned GetOrderOfElements()
    {
        return mOrderOfElements;
    }
    unsigned GetOrderOfBoundaryElements()
    {
        return mOrderOfBoundaryElements;
    }

    bool GetReadContainingElementOfBoundaryElement()
    {
        return mReadContainingElementOfBoundaryElement;
    }

    std::vector<double> GetNodeAttributes();

    std::vector<double> GetNode(unsigned index);

    ElementData GetElementData(unsigned index);

    ElementData GetFaceData(unsigned index);

    std::vector<unsigned> GetContainingElementIndices(unsigned index);


    /*** Returns true if reading binary files, false if reading ascii files */
    bool IsFileFormatBinary();

    bool HasNclFile();

    void SetReadBufferSize(unsigned bufferSize);

    void SetNodePermutation(std::vector<unsigned>& rPermutationVector);

private:

    void OpenFiles();

    void OpenNodeFile();

    void OpenElementsFile();

    void OpenFacesFile();

    void OpenNclFile();

    void OpenCableElementsFile();

    void ReadHeaders();

    void CloseFiles();

    void GetNextLineFromStream(std::ifstream& rFileStream, std::string& rRawLine);

    template<class T_DATA, class T_ATTR>
    void GetNextItemFromStream(std::ifstream& rFileStream, unsigned expectedItemNumber,
                               std::vector<T_DATA>& rDataPacket, const unsigned& rNumAttributes, std::vector<T_ATTR>& rAttributes);

    std::string GetMeshFileBaseName();

    void GetOneDimBoundary();

    void EnsureIndexingFromZero(std::vector<unsigned>& rNodeIndices);

};

#endif //_TRIANGLESMESHREADER_HPP_