AbstractHdf5Converter.cpp

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*/
 
#include "AbstractHdf5Converter.hpp"
#include "Version.hpp"
 
 
/*
 * Operator function to be called by H5Literate [HDF5 1.8.x] or H5Giterate [HDF5 1.6.x] (in TestListingDatasetsInAnHdf5File).
 */
herr_t op_func (hid_t loc_id,
                const char *name,
                const H5L_info_t *info,
                void *operator_data);
 
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractHdf5Converter<ELEMENT_DIM, SPACE_DIM>::AbstractHdf5Converter(const FileFinder& rInputDirectory,
                                                                     const std::string& rFileBaseName,
                                                                     AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>* pMesh,
                                                                     const std::string& rSubdirectoryName,
                                                                     unsigned precision)
    : mrH5Folder(rInputDirectory),
      mFileBaseName(rFileBaseName),
      mOpenDatasetIndex(UNSIGNED_UNSET),
      mpMesh(pMesh),
      mRelativeSubdirectory(rSubdirectoryName),
      mPrecision(precision)
{
    GenerateListOfDatasets(mrH5Folder, mFileBaseName);
 
    // Create new directory in which to store everything
    FileFinder sub_directory(mRelativeSubdirectory, mrH5Folder);
    mpOutputFileHandler = new OutputFileHandler(sub_directory, false);
 
    MoveOntoNextDataset();
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractHdf5Converter<ELEMENT_DIM, SPACE_DIM>::WriteInfoFile()
{
    // Note that we don't want the child processes to write info files
    if (PetscTools::AmMaster())
    {
        std::string time_info_filename;
 
        // If the dataset is just "Data" then we will leave the original filename as it is (to avoid confusion!)
        // If the dataset is a new variant like "Postprocessing" then we will put the dataset name in the output.
        if (mDatasetNames[mOpenDatasetIndex]=="Data")
        {
           time_info_filename = mFileBaseName + "_times.info";
        }
        else
        {
           time_info_filename = mDatasetNames[mOpenDatasetIndex] + "_times.info";
        }
        out_stream p_file = mpOutputFileHandler->OpenOutputFile(time_info_filename);
 
        std::vector<double> time_values = mpReader->GetUnlimitedDimensionValues();
        unsigned num_timesteps = time_values.size();
        double first_timestep = time_values.front();
        double last_timestep = time_values.back();
 
        double timestep = num_timesteps > 1 ? time_values[1] - time_values[0] : DOUBLE_UNSET;
 
        *p_file << "Number of timesteps " << num_timesteps << std::endl;
        *p_file << "timestep " << timestep << std::endl;
        *p_file << "First timestep " << first_timestep << std::endl;
        *p_file << "Last timestep " << last_timestep << std::endl;
        *p_file << ChasteBuildInfo::GetProvenanceString();
 
        p_file->close();
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractHdf5Converter<ELEMENT_DIM,SPACE_DIM>::~AbstractHdf5Converter()
{
    delete mpOutputFileHandler;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::string AbstractHdf5Converter<ELEMENT_DIM,SPACE_DIM>::GetSubdirectory()
{
    return mRelativeSubdirectory;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractHdf5Converter<ELEMENT_DIM,SPACE_DIM>::MoveOntoNextDataset()
{
    // If we are already at the end just return false.
    if (mDatasetNames.size() == mOpenDatasetIndex+1u)
    {
        return false;
    }
 
    // If we haven't read anything yet, start at the beginning, otherwise increment by one.
    if (mOpenDatasetIndex==UNSIGNED_UNSET)
    {
        mOpenDatasetIndex = 0u;
    }
    else
    {
        mOpenDatasetIndex++;
    }
 
    // Store directory, mesh and filenames and create the reader
    mpReader.reset(new Hdf5DataReader(mrH5Folder, mFileBaseName, mDatasetNames[mOpenDatasetIndex]));
 
    // Check the data file for basic validity
    std::vector<std::string> variable_names = mpReader->GetVariableNames();
    mNumVariables = variable_names.size();
 
    if (mpReader->GetNumberOfRows() != mpMesh->GetNumNodes())
    {
        delete mpOutputFileHandler;
        EXCEPTION("Mesh and HDF5 file have a different number of nodes");
    }
    WriteInfoFile();
 
    return true;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractHdf5Converter<ELEMENT_DIM,SPACE_DIM>::GenerateListOfDatasets(const FileFinder& rH5Folder,
                                                                          const std::string& rFileName)
{
    /*
     * Open file.
     */
    std::string file_name = rH5Folder.GetAbsolutePath() + rFileName + ".h5";
    hid_t file = H5Fopen(file_name.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
 
    /*
     * Begin HDF5 iteration, calls a method that populates mDatasetNames.
     */
    H5Literate(file, H5_INDEX_NAME, H5_ITER_NATIVE, nullptr, op_func, &mDatasetNames);
 
    H5Fclose(file);
 
    // Remove datasets that end in "_Unlimited", as these are paired up with other ones!
    std::string ending = "_Unlimited";
 
    // Strip off the independent variables from the list
    std::vector<std::string>::iterator iter;
    for (iter = mDatasetNames.begin(); iter != mDatasetNames.end(); )
    {
        // If the dataset name is "Time" OR ...
        // it is longer than the ending we are looking for ("_Unlimited") ...
        // ... AND it ends with the string we are looking for,
        // then erase it.
        if ((*(iter) == "Time") ||
            ((iter->length() > ending.length()) &&
            (0 == iter->compare(iter->length() - ending.length(), ending.length(), ending))))
        {
            iter = mDatasetNames.erase(iter);
        }
        else
        {
            ++iter;
        }
    }
}
 
/*
 * HDF5 Operator function.
 *
 * Puts the name of the objects (in this case 'datasets')
 * in an HDF5 file into a std::vector for us to use for
 * iterating over the file.
 *
 * This was based on a couple of HDF5 example files.
 */
herr_t op_func (hid_t loc_id, const char *name,
                const H5L_info_t *info,
                void *operator_data)
{
    std::vector<std::string>* p_dataset_names = static_cast<std::vector< std::string > * >(operator_data);
 
    /*
     * Get type of the object and display its name and type.
     * The name of the object is passed to this function by
     * the Library.
     */
    H5O_info_t infobuf;
    H5Oget_info_by_name (loc_id, name, &infobuf, H5P_DEFAULT);
    switch (infobuf.type)
    {
//          case H5O_TYPE_GROUP:
//              printf ("  Group: %s\n", name);
//              break;
        case H5O_TYPE_DATASET:
            p_dataset_names->push_back(name);
            break;
//          case H5O_TYPE_NAMED_DATATYPE:
//              printf ("  Datatype: %s\n", name);
//              break;
        default:
            NEVER_REACHED;
            // If you ever do reach here, it means that an HDF5 file you are trying to convert contains
            // something other than a 'Dataset', which is the usual data structure we write out in Chaste.
            // The above commented out lines should help you figure out what it is, and how it got there.
    }
    return 0;
}
 
// Explicit instantiation
template class AbstractHdf5Converter<1,1>;
template class AbstractHdf5Converter<1,2>;
template class AbstractHdf5Converter<2,2>;
template class AbstractHdf5Converter<1,3>;
template class AbstractHdf5Converter<2,3>;
template class AbstractHdf5Converter<3,3>;