// private readonly ReaderWriterLockSlim lock_ = new ReaderWriterLockSlim();
public Hdf5AcquisitionFileWriter(string filename, string groupName = "ROOT")
{
H5E.set_auto(H5E.DEFAULT, null, IntPtr.Zero);
//lock_.EnterWriteLock();
_filename = filename;
fileId = Hdf5.CreateFile(filename);
_groupName = groupName;
_groupId = Hdf5.CreateOrOpenGroup(fileId, Hdf5Utils.NormalizedName(_groupName));
Header = new Hdf5AcquisitionFile();
_nrOfRecords = 0;
_sampleCount = 0;
//lock_.ExitWriteLock();
}
public void SaveHeader()
{
//lock_.EnterWriteLock();
Trace.WriteLine($"saving file {Header.Patient.Name} samples: {_sampleCount}; fileId: {fileId}");
Header.Recording.EndTime = Header.Recording.StartTime + TimeSpan.FromSeconds(_sampleCount / Header.Recording.SampleRate);
Header.Recording.NrOfSamples = _sampleCount;
Header.EventListToEvents();
for (int i = 0; i < Header.Channels.Count(); i++)
{
Header.Channels[i].NrOfSamples = _sampleCount;
}
Trace.WriteLine($"writing file {Header.Patient.Name} groupId: {_groupId}; fileId: {fileId}");
Hdf5.WriteObject(_groupId, Header);
//lock_.ExitWriteLock();
}
public static bool WriteAttributeByPath(string fileName, string xpath, string attributeName, string value)
{
long fileId = -1;
try
{
var fileStructure = Hdf5.ReadFlatFileStructure(fileName);
fileId = Hdf5.OpenFile(fileName, true);
if (fileId <= 0)
{
LogMessage("Invalid type", Hdf5LogLevel.Error);
return(false);
}
var group = fileStructure.SingleOrDefault(element => element.Name == xpath);
if (group == null)
{
LogMessage($"group {xpath} was not found", Hdf5LogLevel.Error);
return(false);
}
var groupAccessId = H5G.open(fileId, group.Name);
if (groupAccessId <= 0)
{
LogMessage($"unable to open group", Hdf5LogLevel.Error);
return(false);
}
var result = Hdf5.WriteAttribute(groupAccessId, attributeName, value);
return(result.success >= 0);
}
catch (Exception e)
{
LogMessage($"Error reading Attribute: {e.Message}", Hdf5LogLevel.Error);
return(false);
}
finally
{
if (fileId > 0)
{
H5F.close(fileId);
}
}
}
/// <summary>
/// Initializes a new instance of the <see cref="Hdf5AcquisitionFileReader"/> class.
/// </summary>
/// <param name="filename">A filename.</param>
/// <param name="labels"></param>
/// <param name="groupName">a root group. If not specified used "ROOT</param>
public Hdf5AcquisitionFileReader(string filename, string[] labels = null, string groupName = "ROOT")
{
fileId = Hdf5.OpenFile(filename, readOnly: true);
_header = Hdf5.ReadObject <Hdf5AcquisitionFile>(fileId, groupName);
_groupName = groupName;
_usedChannels = new Dictionary <string, short>();
for (short i = 0; i < _header.Recording.NrOfChannels; i++)
{
_usedChannels.Add(_header.Channels[i].Label, i);
}
if (labels == null)
{
_labels = _header.Channels.Select(c => c.Label).ToList();
}
else
{
_labels = labels;
}
_readChannelCnt = _labels.Count;
_signals = new List <short[]>(_readChannelCnt);
}
public (int success, long CreatedId) WriteArray(long groupId, string name, Array collection, Dictionary <string, List <string> > attributes)
{
Type type = collection.GetType();
Type elementType = type.GetElementType();
TypeCode typeCode = Type.GetTypeCode(elementType);
(int success, long CreatedId)result;
switch (typeCode)
{
case TypeCode.Boolean:
var bls = collection.ConvertArray <bool, ushort>(Convert.ToUInt16);
result = rw.WriteFromArray <ushort>(groupId, name, bls);
break;
case TypeCode.Byte:
result = rw.WriteFromArray <byte>(groupId, name, collection);
break;
case TypeCode.Char:
var chrs = collection.ConvertArray <char, ushort>(Convert.ToUInt16);
result = rw.WriteFromArray <ushort>(groupId, name, chrs);
break;
case TypeCode.DateTime:
var dts = collection.ConvertArray <DateTime, long>(dt => Hdf5Conversions.FromDatetime(dt, Hdf5.Settings.DateTimeType));
result = rw.WriteFromArray <long>(groupId, name, dts);
break;
case TypeCode.Decimal:
var decs = collection.ConvertArray <decimal, double>(Convert.ToDouble);
result = rw.WriteFromArray <double>(groupId, name, decs);
break;
case TypeCode.Double:
result = rw.WriteFromArray <double>(groupId, name, collection);
break;
case TypeCode.Int16:
result = rw.WriteFromArray <short>(groupId, name, collection);
break;
case TypeCode.Int32:
result = rw.WriteFromArray <int>(groupId, name, collection);
break;
case TypeCode.Int64:
result = rw.WriteFromArray <long>(groupId, name, collection);
break;
case TypeCode.SByte:
result = rw.WriteFromArray <sbyte>(groupId, name, collection);
break;
case TypeCode.Single:
result = rw.WriteFromArray <float>(groupId, name, collection);
break;
case TypeCode.UInt16:
result = rw.WriteFromArray <ushort>(groupId, name, collection);
break;
case TypeCode.UInt32:
result = rw.WriteFromArray <uint>(groupId, name, collection);
break;
case TypeCode.UInt64:
result = rw.WriteFromArray <ulong>(groupId, name, collection);
break;
case TypeCode.String:
if (collection.Rank > 1 && collection.GetLength(1) > 1)
{
throw new Hdf5Exception("Only 1 dimensional string arrays allowed: " + name);
}
result = rw.WriteStrings(groupId, name, (string[])collection);
break;
default:
if (elementType == typeof(TimeSpan))
{
var tss = collection.ConvertArray <TimeSpan, long>(dt => dt.Ticks);
result = rw.WriteFromArray <long>(groupId, name, tss);
}
else
{
string str = "type is not supported: ";
throw new NotSupportedException(str + elementType.FullName);
}
break;
}
if (result.success == 0)//append attributes
{
foreach (KeyValuePair <string, List <string> > entry in attributes)
{
Hdf5.WriteStringAttribute(groupId, entry.Key, string.Join("',", entry.Value), name);
}
}
return(result);
}