Hdf5DataReader.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 HDF5DATAREADER_HPP_
#define HDF5DATAREADER_HPP_

#ifndef H5_USE_16_API
#define H5_USE_16_API 1
#endif

#include <hdf5.h>
#include <petscvec.h>
#include <string>
#include <vector>
#include <map>

#include "FileFinder.hpp"

const unsigned MAX_STRING_SIZE = 100; 

class Hdf5DataReader
{
private:

    static const unsigned MAX_DATASET_RANK = 3;             
    std::string mDirectory;                                 
    std::string mBaseName;                                  
    hid_t mFileId;                                          
    hid_t mVariablesDatasetId;                              
    unsigned mVariablesDatasetRank;                         
    hsize_t mVariablesDatasetSizes[MAX_DATASET_RANK];       
    bool mIsUnlimitedDimensionSet;                          
    hid_t mTimeDatasetId;                                   
    hsize_t mNumberTimesteps;                               
    std::vector<std::string> mVariableNames;                
    std::map<std::string, unsigned> mVariableToColumnIndex; 
    std::map<std::string, std::string> mVariableToUnit;     
    bool mIsDataComplete;                                   
    std::vector<unsigned> mIncompleteNodeIndices;           
    bool mClosed;                                           
    void CommonConstructor(const FileFinder& rDirectory,
                           const std::string& rBaseName);

public:

    Hdf5DataReader(const std::string& rDirectory,
                   const std::string& rBaseName,
                   bool makeAbsolute=true);

    Hdf5DataReader(const FileFinder& rDirectory,
                   const std::string& rBaseName);

    std::vector<double> GetVariableOverTime(const std::string& rVariableName,
                                            unsigned nodeIndex);

    std::vector<std::vector<double> > GetVariableOverTimeOverMultipleNodes(const std::string& rVariableName,
                                                                           unsigned lowerIndex,
                                                                           unsigned upperIndex);

    void GetVariableOverNodes(Vec data, const std::string& rVariableName, unsigned timestep=0);

    std::vector<double> GetUnlimitedDimensionValues();

    unsigned GetNumberOfRows();

    std::vector<std::string> GetVariableNames();

    std::string GetUnit(const std::string& rVariableName);

    bool IsDataComplete();

    std::vector<unsigned> GetIncompleteNodeMap();

    void Close();

    ~Hdf5DataReader();
};

#endif /*HDF5DATAREADER_HPP_*/