Hdf5DataWriter.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 HDF5DATAWRITER_HPP_
#define HDF5DATAWRITER_HPP_

#include <string>
#include <vector>

#include "Hdf5DataReader.hpp" //For common definitions
#include "DataWriterVariable.hpp"
#include "DistributedVectorFactory.hpp"

class Hdf5DataWriter//  : public AbstractDataWriter
{
private:

    DistributedVectorFactory& mrVectorFactory;
    std::string mDirectory; 
    std::string mBaseName; 
    bool mCleanDirectory;   
    bool mIsInDefineMode; 
    bool mIsFixedDimensionSet; 
    bool mIsUnlimitedDimensionSet; 
    std::string mUnlimitedDimensionName; 
    std::string mUnlimitedDimensionUnit; 
    unsigned mEstimatedUnlimitedLength; 
    unsigned mFileFixedDimensionSize; 
    unsigned mDataFixedDimensionSize; 
    unsigned mLo; 
    unsigned mHi; 
    unsigned mNumberOwned; 
    unsigned mOffset; 
    bool mIsDataComplete; 
    bool mNeedExtend; 
    std::vector<unsigned> mIncompleteNodeIndices; 
    bool mUseMatrixForIncompleteData; 
    std::vector<DataWriterVariable> mVariables; 
    hid_t mFileId; 
    hid_t mDatasetId; 
    hid_t mTimeDatasetId; 
    long mCurrentTimeStep; 
    static const unsigned DATASET_DIMS=3; 
    hsize_t mDatasetDims[DATASET_DIMS]; 
    Mat mSinglePermutation; 
    Mat mDoublePermutation;
    Mat mSingleIncompleteOutputMatrix; 
    Mat mDoubleIncompleteOutputMatrix; 
    bool mUseOptimalChunkSizeAlgorithm; 
    unsigned mFixedChunkSize; 
    void CheckVariableName(const std::string& rName);

    void CheckUnitsName(const std::string& rName);

    void ComputeIncompleteOffset();

public:

    Hdf5DataWriter(DistributedVectorFactory& rVectorFactory,
                   const std::string& rDirectory,
                   const std::string& rBaseName,
                   bool cleanDirectory=true,
                   bool extendData=false);

    virtual ~Hdf5DataWriter();

    void DefineFixedDimension(long dimensionSize);

    void DefineFixedDimension(const std::vector<unsigned>& rNodesToOuput, long vecSize);

    void DefineUnlimitedDimension(const std::string& rVariableName, const std::string& rVariableUnits, unsigned estimatedLength = 1);

    void AdvanceAlongUnlimitedDimension();

    int DefineVariable(const std::string& rVariableName, const std::string& rVariableUnits);

    virtual void EndDefineMode();

    void PossiblyExtend();

    void PutVector(int variableID, Vec petscVector);

    void PutStripedVector(std::vector<int> variableIDs, Vec petscVector);

    void PutUnlimitedVariable(double value);

    void Close();

    int GetVariableByName(const std::string& rVariableName);


    bool ApplyPermutation(const std::vector<unsigned>& rPermutation);

    void DefineFixedDimensionUsingMatrix(const std::vector<unsigned>& rNodesToOuput, long vecSize);

    void SetFixedChunkSize(unsigned chunkSize);
};

#endif /*HDF5DATAWRITER_HPP_*/