Hdf5DataWriter.hpp

00001 /*
00002 
00003 Copyright (C) University of Oxford, 2005-2011
00004 
00005 University of Oxford means the Chancellor, Masters and Scholars of the
00006 University of Oxford, having an administrative office at Wellington
00007 Square, Oxford OX1 2JD, UK.
00008 
00009 This file is part of Chaste.
00010 
00011 Chaste is free software: you can redistribute it and/or modify it
00012 under the terms of the GNU Lesser General Public License as published
00013 by the Free Software Foundation, either version 2.1 of the License, or
00014 (at your option) any later version.
00015 
00016 Chaste is distributed in the hope that it will be useful, but WITHOUT
00017 ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
00018 FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
00019 License for more details. The offer of Chaste under the terms of the
00020 License is subject to the License being interpreted in accordance with
00021 English Law and subject to any action against the University of Oxford
00022 being under the jurisdiction of the English Courts.
00023 
00024 You should have received a copy of the GNU Lesser General Public License
00025 along with Chaste. If not, see <http://www.gnu.org/licenses/>.
00026 
00027 */
00028 #ifndef HDF5DATAWRITER_HPP_
00029 #define HDF5DATAWRITER_HPP_
00030 
00031 #include <string>
00032 #include <vector>
00033 
00034 #include "Hdf5DataReader.hpp" //For common definitions
00035 #include "DataWriterVariable.hpp"
00036 #include "DistributedVectorFactory.hpp"
00037 
00038 
00039 
00043 class Hdf5DataWriter//  : public AbstractDataWriter
00044 {
00045 private:
00047     DistributedVectorFactory& mrVectorFactory;
00048     std::string mDirectory; 
00049     std::string mBaseName; 
00050     bool mCleanDirectory;   
00051     bool mIsInDefineMode; 
00052     bool mIsFixedDimensionSet; 
00053     bool mIsUnlimitedDimensionSet; 
00054     std::string mUnlimitedDimensionName; 
00055     std::string mUnlimitedDimensionUnit; 
00056     unsigned mEstimatedUnlimitedLength; 
00057     unsigned mFileFixedDimensionSize; 
00058     unsigned mDataFixedDimensionSize; 
00059     unsigned mLo; 
00060     unsigned mHi; 
00061     unsigned mNumberOwned; 
00062     unsigned mOffset; 
00063     bool mIsDataComplete; 
00064     bool mNeedExtend; 
00065     std::vector<unsigned> mIncompleteNodeIndices; 
00066     bool mUseMatrixForIncompleteData; 
00068     std::vector<DataWriterVariable> mVariables; 
00070     hid_t mFileId; 
00071     hid_t mDatasetId; 
00072     hid_t mTimeDatasetId; 
00074     long mCurrentTimeStep; 
00076     static const unsigned DATASET_DIMS=3; 
00077     hsize_t mDatasetDims[DATASET_DIMS]; 
00079     Mat mSinglePermutation; 
00080     Mat mDoublePermutation;
00082     Mat mSingleIncompleteOutputMatrix; 
00083     Mat mDoubleIncompleteOutputMatrix; 
00085     bool mUseOptimalChunkSizeAlgorithm; 
00086     unsigned mFixedChunkSize; 
00093     void CheckVariableName(const std::string& rName);
00094 
00100     void CheckUnitsName(const std::string& rName);
00101 
00105     void ComputeIncompleteOffset();
00106 
00107 public:
00108 
00122     Hdf5DataWriter(DistributedVectorFactory& rVectorFactory,
00123                    const std::string& rDirectory,
00124                    const std::string& rBaseName,
00125                    bool cleanDirectory=true,
00126                    bool extendData=false);
00127 
00131     virtual ~Hdf5DataWriter();
00132 
00138     void DefineFixedDimension(long dimensionSize);
00139 
00146     void DefineFixedDimension(const std::vector<unsigned>& rNodesToOuput, long vecSize);
00147 
00156     void DefineUnlimitedDimension(const std::string& rVariableName, const std::string& rVariableUnits, unsigned estimatedLength = 1);
00157 
00162     void AdvanceAlongUnlimitedDimension();
00163 
00172     int DefineVariable(const std::string& rVariableName, const std::string& rVariableUnits);
00173 
00177     virtual void EndDefineMode();
00178 
00182     void PossiblyExtend();
00183 
00190     void PutVector(int variableID, Vec petscVector);
00191 
00198     void PutStripedVector(std::vector<int> variableIDs, Vec petscVector);
00199 
00205     void PutUnlimitedVariable(double value);
00206 
00210     void Close();
00211 
00219     int GetVariableByName(const std::string& rVariableName);
00220     
00221     
00228     bool ApplyPermutation(const std::vector<unsigned>& rPermutation);
00229     
00237     void DefineFixedDimensionUsingMatrix(const std::vector<unsigned>& rNodesToOuput, long vecSize);
00238 
00245     void SetFixedChunkSize(unsigned chunkSize);
00246 
00247 };
00248 
00249 #endif /*HDF5DATAWRITER_HPP_*/

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