AbstractHdf5Access.cpp

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*/

#include "Exception.hpp"
#include "AbstractHdf5Access.hpp"

bool AbstractHdf5Access::DoesDatasetExist(const std::string& rDatasetName)
{
#if H5_VERS_MAJOR>=1 && H5_VERS_MINOR>=8
    // This is a nice method for testing existence, introduced in HDF5 1.8.0
    htri_t dataset_status = H5Lexists(mFileId, rDatasetName.c_str(), H5P_DEFAULT);
    return (dataset_status>0);
#else
    bool result=false;
    // This is not a nice way of doing it because the error stack produces a load of 'HDF failed' output.
    // The "TRY" macros are a convenient way to temporarily turn the error stack off.
    H5E_BEGIN_TRY
    {
        hid_t dataset_id = H5Dopen(mFileId, rDatasetName.c_str());
        if (dataset_id>0)
        {
            H5Dclose(dataset_id);
            result = true;
        }
    }
    H5E_END_TRY;

    return result;
#endif
}

void AbstractHdf5Access::SetUnlimitedDatasetId()
{
    // Now deal with the unlimited dimension

    // In terms of an Unlimited dimension dataset:
    // * Files pre - r16738 (inc. Release 3.1 and earlier) use simply "Time" for "Data"'s unlimited variable.
    // * Files generated by r16738 - r18257 used "<DatasetName>_Time" for "<DatasetName>"'s unlimited variable,
    //   - These are not to be used and there is no backwards compatibility for them, since they weren't in a release.
    // * Files post r18257 (inc. Release 3.2 onwards) use "<DatasetName>_Unlimited" for "<DatasetName>"'s
    //   unlimited variable,
    //   - a new attribute "Name" has been added to the Unlimited Dataset to allow it to assign
    //     any name to the unlimited variable. Which can then be easily read by Hdf5DataReader.
    //   - if this dataset is missing we look for simply "Time" to remain backwards compatible with Releases <= 3.1

    if (DoesDatasetExist(mDatasetName + "_Unlimited"))
    {
        mUnlimitedDatasetId = H5Dopen(mFileId, (mDatasetName + "_Unlimited").c_str());
        hid_t name_attribute_id = H5Aopen_name(mUnlimitedDatasetId, "Name");
        hid_t unit_attribute_id = H5Aopen_name(mUnlimitedDatasetId, "Unit");

        hid_t attribute_type  = H5Aget_type(name_attribute_id);

        // Read into it.
        char* string_array = (char *)malloc(sizeof(char)*MAX_STRING_SIZE);
        H5Aread( name_attribute_id, attribute_type, string_array);
        std::string name_string(&string_array[0]);
        mUnlimitedDimensionName = name_string;

        H5Aread( unit_attribute_id, attribute_type, string_array);
        std::string unit_string(&string_array[0]);
        mUnlimitedDimensionUnit = unit_string;

        free(string_array);
        H5Tclose(attribute_type);
        H5Aclose(name_attribute_id);
        H5Aclose(unit_attribute_id);
    }
    else if (DoesDatasetExist("Time"))
    {
        mUnlimitedDimensionName = "Time";
        mUnlimitedDimensionUnit = "msec";
        mUnlimitedDatasetId = H5Dopen(mFileId, mUnlimitedDimensionName.c_str());
    }
    else
    {
        NEVER_REACHED;
    }
    mIsUnlimitedDimensionSet = true;
}

AbstractHdf5Access::AbstractHdf5Access(const std::string& rDirectory,
                   const std::string& rBaseName,
                   const std::string& rDatasetName,
                   bool makeAbsolute)
 : mBaseName(rBaseName),
   mDatasetName(rDatasetName),
   mIsDataComplete(true),
   mIsUnlimitedDimensionSet(false)
{
    RelativeTo::Value relative_to;
    if (makeAbsolute)
    {
        relative_to = RelativeTo::ChasteTestOutput;
    }
    else
    {
        relative_to = RelativeTo::Absolute;
    }
    mDirectory.SetPath(rDirectory, relative_to);
}

AbstractHdf5Access::AbstractHdf5Access(const FileFinder& rDirectory,
                                       const std::string& rBaseName,
                                       const std::string& rDatasetName)
 : mBaseName(rBaseName),
   mDatasetName(rDatasetName),
   mDirectory(rDirectory),
   mIsDataComplete(true),
   mIsUnlimitedDimensionSet(false)
{
}

AbstractHdf5Access::~AbstractHdf5Access()
{
}


bool AbstractHdf5Access::IsDataComplete()
{
    return mIsDataComplete;
}


std::vector<unsigned> AbstractHdf5Access::GetIncompleteNodeMap()
{
    return mIncompleteNodeIndices;
}

std::string AbstractHdf5Access::GetUnlimitedDimensionName()
{
    return mUnlimitedDimensionName;
}

std::string AbstractHdf5Access::GetUnlimitedDimensionUnit()
{
    return mUnlimitedDimensionUnit;
}

void AbstractHdf5Access::SetMainDatasetRawChunkCache()
{
    // 128 M cache for raw data. 12799 is a prime number which is 100 x larger
    // than the number of 1 MB chunks (the largest we have tested with) which
    // could fit into the 128 M cache. 0.75 for the last argument is the default.
    // See: http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetChunkCache

    hsize_t max_objects_in_chunk_cache = 12799u;
    hsize_t max_bytes_in_cache = 128u*1024u*1024u;
#if H5_VERS_MAJOR>=1 && H5_VERS_MINOR>=8 && H5_VERS_RELEASE>=3 // HDF5 1.8.3+
    // These methods set the cache on a dataset basis
    hid_t dapl_id = H5Dget_access_plist( mVariablesDatasetId );
    H5Pset_chunk_cache( dapl_id,
                        max_objects_in_chunk_cache ,
                        max_bytes_in_cache ,
                        H5D_CHUNK_CACHE_W0_DEFAULT);
#else
    // These older methods set the cache on a file basis
    hid_t fapl_id = H5Fget_access_plist( mFileId );
    H5Pset_cache( fapl_id,
                  0, // unused
                  max_objects_in_chunk_cache,
                  max_bytes_in_cache,
                  0.75); // default value
#endif
}