Hdf5DataWriter.hpp

/*

Copyright (c) 2005-2012, University of Oxford.
All rights reserved.

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.

Redistribution and use in source and binary forms, with or without
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
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   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
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/

#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_*/