Hdf5DataReader.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 HDF5DATAREADER_HPP_
00029 #define HDF5DATAREADER_HPP_
00030 
00031 #ifndef H5_USE_16_API
00032 #define H5_USE_16_API 1
00033 #endif
00034 
00035 #include <hdf5.h>
00036 #include <petscvec.h>
00037 #include <string>
00038 #include <vector>
00039 #include <map>
00040 
00041 #include "FileFinder.hpp"
00042 
00043 const unsigned MAX_STRING_SIZE = 100; 
00044 
00045 
00049 class Hdf5DataReader
00050 {
00051 private:
00052 
00053     static const unsigned MAX_DATASET_RANK = 3;             
00055     std::string mDirectory;                                 
00056     std::string mBaseName;                                  
00058     hid_t mFileId;                                          
00060     hid_t mVariablesDatasetId;                              
00061     unsigned mVariablesDatasetRank;                         
00062     hsize_t mVariablesDatasetSizes[MAX_DATASET_RANK];       
00064     bool mIsUnlimitedDimensionSet;                          
00065     hid_t mTimeDatasetId;                                   
00066     hsize_t mNumberTimesteps;                               
00068     std::vector<std::string> mVariableNames;                
00069     std::map<std::string, unsigned> mVariableToColumnIndex; 
00070     std::map<std::string, std::string> mVariableToUnit;     
00072     bool mIsDataComplete;                                   
00073     std::vector<unsigned> mIncompleteNodeIndices;           
00081     void CommonConstructor(const FileFinder& rDirectory,
00082                            const std::string& rBaseName);
00083 
00084 public:
00085 
00094     Hdf5DataReader(const std::string& rDirectory,
00095                    const std::string& rBaseName,
00096                    bool makeAbsolute=true);
00097 
00104     Hdf5DataReader(const FileFinder& rDirectory,
00105                    const std::string& rBaseName);
00106 
00113     std::vector<double> GetVariableOverTime(const std::string& rVariableName,
00114                                             unsigned nodeIndex);
00115 
00123     void GetVariableOverNodes(Vec data, const std::string& rVariableName, unsigned timestep=0);
00124 
00128     std::vector<double> GetUnlimitedDimensionValues();
00129 
00133     unsigned GetNumberOfRows();
00134 
00138     std::vector<std::string> GetVariableNames();
00139 
00145     std::string GetUnit(const std::string& rVariableName);
00146 
00150     bool IsDataComplete();
00151 
00155     std::vector<unsigned> GetIncompleteNodeMap();
00156 
00160     void Close();
00161 
00165     ~Hdf5DataReader();
00166 
00167 };
00168 
00169 #endif /*HDF5DATAREADER_HPP_*/

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