public KamaAcquisitionFile(string filename, AcquisitionInterface acquisitionInterface, ILogger logger,
int eitDefaultChunkSize = 24000, int ecgDefaultChunkSize = 10)
{
FileName = filename;
Logger = logger;
EITDefaultChunkSize = eitDefaultChunkSize;
ECGDefaultChunkSize = ecgDefaultChunkSize;
RecordNumber = 1;
H5E.set_auto(H5E.DEFAULT, null, IntPtr.Zero);
fileId = Hdf5.CreateFile(filename);
groupRoot = fileId;
groupEIT = Hdf5.CreateOrOpenGroup(groupRoot, "eit");
ProcedureInformation = new ProcedureInformation(fileId, groupRoot, logger)
{
ProcedureDirectory = Path.GetDirectoryName(filename),
StartDateTime = DateTime.Now,
EndDateTime = DateTime.Now
};
SystemInformation = new SystemInformation(fileId, groupRoot, logger);
SystemInformation.SystemType = acquisitionInterface.ToString();
// InjectionGroup = new InjectionGroup(fileId, groupRoot);
CalibrationGroup = new CalibrationGroup(fileId, groupRoot, logger);
SystemEvents = new SystemEventGroup(fileId, groupRoot, logger);
RPosition = new RPositionGroup(fileId, groupRoot, logger);
Tags = new TagsGroup(fileId, groupRoot, logger);
UserEventsGroup = new UserEventsGroup(fileId, groupRoot, logger);
}
public void H5Eset_autoTest1()
{
H5E.auto_t cb = null;
IntPtr client_data = IntPtr.Zero;
Assert.IsTrue(
H5E.set_auto(H5E.DEFAULT, cb, client_data) >= 0);
}
public bool EnableErrorReporting(bool enable)
{
ErrorLoggingEnable = enable;
if (enable)
{
return(H5E.set_auto(H5E.DEFAULT, Hdf5Errors.ErrorDelegateMethod, IntPtr.Zero) >= 0);
}
return(H5E.set_auto(H5E.DEFAULT, null, IntPtr.Zero) >= 0);
}
public void H5EwalkTest1()
{
H5E.auto_t auto_cb = ErrorDelegateMethod;
Assert.IsTrue(
H5E.set_auto(H5E.DEFAULT, auto_cb, IntPtr.Zero) >= 0);
H5E.walk_t walk_cb = WalkDelegateMethod;
Assert.IsTrue(
H5E.walk(H5E.DEFAULT, H5E.direction_t.H5E_WALK_DOWNWARD,
walk_cb, IntPtr.Zero) >= 0);
}
// 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.CreateGroup(fileId, Hdf5Utils.NormalizedName(_groupName));
Header = new Hdf5AcquisitionFile();
_nrOfRecords = 0;
_sampleCount = 0;
//lock_.ExitWriteLock();
}
// private readonly ReaderWriterLockSlim lock_ = new ReaderWriterLockSlim();
public Hdf5AcquisitionFileWriter(string aFilename, string groupName = "/EEG")
{
H5E.set_auto(H5E.DEFAULT, null, IntPtr.Zero);
//lock_.EnterWriteLock();
_filename = aFilename;
fileId = Hdf5.CreateFile(aFilename);
_groupName = groupName;
_groupId = Hdf5.CreateGroup(fileId, _groupName);
Header = new Hdf5AcquisitionFile();
_nrOfRecords = 0;
_sampleCount = 0;
//lock_.ExitWriteLock();
}
public static void SuppressErrors(Action action)
{
H5E.auto_t func;
IntPtr clientData;
func = null;
clientData = IntPtr.Zero;
H5E.get_auto(H5E.DEFAULT, ref func, ref clientData);
H5E.set_auto(H5E.DEFAULT, null, IntPtr.Zero);
action.Invoke();
H5E.set_auto(H5E.DEFAULT, func, clientData);
}
public static void CaptureHdfLibOutput(ITestOutputHelper logger)
{
H5E.set_auto(H5E.DEFAULT, ErrorDelegateMethod, IntPtr.Zero);
int ErrorDelegateMethod(long estack, IntPtr client_data)
{
H5E.walk(estack, H5E.direction_t.H5E_WALK_DOWNWARD, WalkDelegateMethod, IntPtr.Zero);
return(0);
}
int WalkDelegateMethod(uint n, ref H5E.error_t err_desc, IntPtr client_data)
{
logger.WriteLine($"{n}: {err_desc.desc}");
return(0);
}
}
public void H5EwalkTest2()
{
// H5E.set_auto(H5E.DEFAULT, ErrorDelegateMethod, IntPtr.Zero);
Assert.IsTrue(
H5E.set_auto(H5E.DEFAULT, ErrorDelegateMethod, IntPtr.Zero) >= 0);
H5E.walk_t walk_cb = WalkDelegateMethod;
Assert.IsTrue(
H5E.push(H5E.DEFAULT, "hello.c", "sqrt", 77, H5E.ERR_CLS,
H5E.NONE_MAJOR, H5E.NONE_MINOR, "Hello, World!") >= 0);
Assert.IsTrue(
H5E.push(H5E.DEFAULT, "hello.c", "sqr", 78, H5E.ERR_CLS,
H5E.NONE_MAJOR, H5E.NONE_MINOR, "Hello, World!") >= 0);
Assert.IsTrue(
H5E.walk(H5E.DEFAULT, H5E.direction_t.H5E_WALK_DOWNWARD,
walk_cb, IntPtr.Zero) >= 0);
}
public static List <(string Path, string Name)> GetPathSet(long locationId, int maxDepth, bool includeGroups, bool includeDatasets)
{
ulong idx;
List <(string Path, string Name)> datasetPathSet;
H5E.auto_t func;
IntPtr clientData;
idx = default;
datasetPathSet = new List <(string Path, string Name)>();
func = null;
clientData = IntPtr.Zero;
H5E.get_auto(H5E.DEFAULT, ref func, ref clientData);
H5E.set_auto(H5E.DEFAULT, null, IntPtr.Zero);
H5L.iterate(locationId, H5.index_t.NAME, H5.iter_order_t.INC, ref idx, Callback, Marshal.StringToHGlobalAnsi("/"));
H5E.set_auto(H5E.DEFAULT, func, clientData);
return(datasetPathSet);
int Callback(long groupId, IntPtr intPtrName, ref H5L.info_t info, IntPtr intPtrUserData)
{
long datasetId = -1;
ulong idx2 = default;
int level;
string name;
string userData;
H5O.type_t objectType;
name = Marshal.PtrToStringAnsi(intPtrName);
userData = Marshal.PtrToStringAnsi(intPtrUserData);
level = userData.Split("/".ToArray()).Count();
// this is necessary, since H5Oget_info_by_name is slow because it wants verbose object header data
// and H5G_loc_info is not directly accessible
// only chance is to modify source code (H5Oget_info_by_name) or use V2 B-tree
datasetId = H5D.open(groupId, name);
if (datasetId > -1)
{
objectType = H5O.type_t.DATASET;
}
else
{
groupId = H5G.open(groupId, name);
if (groupId > -1)
{
objectType = H5O.type_t.GROUP;
}
else
{
objectType = H5O.type_t.UNKNOWN;
}
}
switch (objectType)
{
case H5O.type_t.GROUP:
if (level <= maxDepth)
{
H5L.iterate(groupId, H5.index_t.NAME, H5.iter_order_t.INC, ref idx2, Callback, Marshal.StringToHGlobalAnsi(GeneralHelper.CombinePath(userData, name)));
if (includeGroups)
{
datasetPathSet.Add((userData, name));
}
H5G.close(groupId);
}
break;
case H5O.type_t.DATASET:
if (includeDatasets)
{
datasetPathSet.Add((userData, name));
}
H5D.close(datasetId);
break;
default:
break;
}
return(0);
}
}
public static void DisableErrorPrinting()
{
H5E.set_auto(H5E.DEFAULT, null, IntPtr.Zero);
}