I have some code that converts an hdf5 file (or folder of hdf5 files) of hdf files into CSVs. When I run it on a folder of hdf5 files, the code randomly throws exceptions part way through a folder conversion. The exceptions are H5GgetObjectNameByIndexException while doing a H5G::iterate to generate a list of dataset names. When the exception occurs, all files thereafter have the same problem. And the file that triggers it is never consistent. The folder that I'm testing on contains 47 hdf files, most are in the 100-2000K range, though two are 125G and 15G. The big ones don't seem to be the trigger.
Each file is handed independently & serially, so there should be no interaction between them. And I've verified that all hdf objects are closed.
The BuildDatasetList and DatasetIterator code are below.
Given the opaque nature of the HDF5DotNet exceptions, I'm not sure where to turn now.
Scott
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/// <summary>
/// Build the internal list of datasets. Ignores Dimension Scales ("_Time")
/// </summary>
/// <param name="source">source file</param>
/// <param name="reason">failure reason</param>
/// <returns>count of datasets found, negative failure</returns>
public int BuildDatasetList(H5FileId source, out string reason)
{
object something = new object();
int startIndex = 0;
string group = "/";
reason = "";
// Iterate the list of groups to build mDatasets
lock (sLocker)
{
try
{
int result = H5G.iterate(source, group, DatasetIterator, something, ref startIndex);
}
catch (Exception ex)
{
reason = "BuildDatasetList " + ex.GetType().ToString() + ": " + ex.Message;
System.Diagnostics.Debug.WriteLine(reason);
return -1;
}
}
// Return
if (mDatasets == null)
System.Diagnostics.Debug.WriteLine("~~~~~~~~~~~~~~~~~ No Datasets found? ~~~~~~~~~~~~~~~~~");
return this.mDatasets == null ? 0 : this.mDatasets.Count;
}
/// <summary>
/// Callback for the H5G.iterate(). Opens Datasets (ignoring "_Time" data scales) and stores them for use.
/// </summary>
/// <param name="group">container group/file</param>
/// <param name="name">object name</param>
/// <param name="parameter">unused</param>
/// <returns>0 to keep looping</returns>
protected int DatasetIterator(H5GroupId group, string name, object parameter)
{
H5ObjectInfo objInfo;
try
{
objInfo = H5O.getInfoByName(group, name);
}
catch (Exception ex)
{
System.Diagnostics.Debug.WriteLine("DatasetIterator (" + name + ") " + ex.GetType().ToString() + ": " + ex.Message);
return 0;
}
if (objInfo.objectType != H5ObjectType.DATASET)
{
return 0;
}
// Filter out "_Time" datasets (time axes)
if (name.EndsWith("_Time"))
return 0;
// Fill in the Dataset name.
if (mDatasets == null)
mDatasets = new List<string>();
lock (mDatasets)
{
mDatasets.Add(name);
}
// return
return 0;
}
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