AbstractHdf5Access.cpp

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*/
 
#include "AbstractHdf5Access.hpp"
#include "Exception.hpp"
 
bool AbstractHdf5Access::DoesDatasetExist(const std::string& rDatasetName)
{
    // 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);
}
 
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(), H5P_DEFAULT);
        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(), H5P_DEFAULT);
    }
    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
}