public void AppendOrCreateDataset(Array dataset)
{
if (_chunkDims == null)
{
_chunkDims = new[]
{ Convert.ToUInt64(dataset.GetLongLength(0)), Convert.ToUInt64(dataset.GetLongLength(1)) };
Rank = dataset.Rank;
_currentDims = GetDims(dataset);
/* Create the data space with unlimited dimensions. */
_spaceId = H5S.create_simple(Rank, _currentDims, _maxDims);
/* Modify dataset creation properties, i.e. enable chunking */
_propId = H5P.create(H5P.DATASET_CREATE);
_status = H5P.set_chunk(_propId, Rank, _chunkDims);
/* Create a new dataset within the file using chunk creation properties. */
_datasetId = H5D.create(GroupId, Hdf5Utils.NormalizedName(Datasetname), _datatype, _spaceId, H5P.DEFAULT, _propId);
/* Write data to dataset */
GCHandle hnd = GCHandle.Alloc(dataset, GCHandleType.Pinned);
_status = H5D.write(_datasetId, _datatype, H5S.ALL, H5S.ALL, H5P.DEFAULT,
hnd.AddrOfPinnedObject());
hnd.Free();
H5S.close(_spaceId);
_spaceId = -1;
}
else
{
AppendDataset(dataset);
}
}
public static (bool success, IEnumerable <string> result) ReadStrings(long groupId, string name, string alternativeName)
{
long datatype = H5T.create(H5T.class_t.STRING, H5T.VARIABLE);
H5T.set_cset(datatype, H5T.cset_t.UTF8);
H5T.set_strpad(datatype, H5T.str_t.NULLTERM);
//name = ToHdf5Name(name);
var datasetId = H5D.open(groupId, Hdf5Utils.NormalizedName(name));
if (datasetId < 0) //does not exist?
{
datasetId = H5D.open(groupId, Hdf5Utils.NormalizedName(alternativeName));
}
if (datasetId <= 0)
{
Hdf5Utils.LogError?.Invoke($"Error reading {groupId}. Name:{name}. AlternativeName:{alternativeName}");
return(false, Array.Empty <string>());
}
long spaceId = H5D.get_space(datasetId);
long count = H5S.get_simple_extent_npoints(spaceId);
H5S.close(spaceId);
var strs = new List <string>();
if (count >= 0)
{
IntPtr[] rdata = new IntPtr[count];
GCHandle hnd = GCHandle.Alloc(rdata, GCHandleType.Pinned);
H5D.read(datasetId, datatype, H5S.ALL, H5S.ALL,
H5P.DEFAULT, hnd.AddrOfPinnedObject());
for (int i = 0; i < rdata.Length; ++i)
{
int len = 0;
while (Marshal.ReadByte(rdata[i], len) != 0)
{
++len;
}
byte[] buffer = new byte[len];
Marshal.Copy(rdata[i], buffer, 0, buffer.Length);
string s = Encoding.UTF8.GetString(buffer);
strs.Add(s);
// H5.free_memory(rdata[i]);
}
hnd.Free();
}
H5T.close(datatype);
H5D.close(datasetId);
return(true, strs);
}
public static (int success, long CreatedgroupId) WriteStrings(long groupId, string name, IEnumerable <string> strs)
{
// create UTF-8 encoded test datasets
long datatype = H5T.create(H5T.class_t.STRING, H5T.VARIABLE);
H5T.set_cset(datatype, H5T.cset_t.ASCII);
H5T.set_strpad(datatype, H5T.str_t.NULLTERM);
int strSz = strs.Count();
long spaceId = H5S.create_simple(1, new[] { (ulong)strSz }, null);
string normalizedName = Hdf5Utils.NormalizedName(name);
var datasetId = Hdf5Utils.GetDatasetId(groupId, normalizedName, datatype, spaceId);
if (datasetId == -1L)
{
return(-1, -1L);
}
GCHandle[] hnds = new GCHandle[strSz];
IntPtr[] wdata = new IntPtr[strSz];
int cntr = 0;
foreach (string str in strs)
{
hnds[cntr] = GCHandle.Alloc(
Encoding.UTF8.GetBytes(str),
GCHandleType.Pinned);
wdata[cntr] = hnds[cntr].AddrOfPinnedObject();
cntr++;
}
var hnd = GCHandle.Alloc(wdata, GCHandleType.Pinned);
var result = H5D.write(datasetId, datatype, H5S.ALL, H5S.ALL,
H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
for (int i = 0; i < strSz; ++i)
{
hnds[i].Free();
}
H5D.close(datasetId);
H5S.close(spaceId);
H5T.close(datatype);
return(result, datasetId);
}
public void AppendOrCreateDataset(Array dataset)
{
if (_chunkDims == null)
{
if (dataset.Rank < 1)
{
string msg = "Empty array was passed. Ignoring.";
Hdf5Utils.LogError?.Invoke(msg);
return;
}
for (int dimension = 1; dimension <= dataset.Rank; dimension++)
{
var size = dataset.GetUpperBound(dimension - 1) + 1;
if (size == 0)
{
string msg = $"Empty array was passed for dimension {dimension}. Ignoring.";
Hdf5Utils.LogError?.Invoke(msg);
return;
}
}
_chunkDims = new[]
{ Convert.ToUInt64(dataset.GetLongLength(0)), Convert.ToUInt64(dataset.GetLongLength(1)) };
Rank = dataset.Rank;
_currentDims = GetDims(dataset);
/* Create the data space with unlimited dimensions. */
_spaceId = H5S.create_simple(Rank, _currentDims, _maxDims);
/* Modify dataset creation properties, i.e. enable chunking */
_propId = H5P.create(H5P.DATASET_CREATE);
_status = H5P.set_chunk(_propId, Rank, _chunkDims);
/* Create a new dataset within the file using chunk creation properties. */
_datasetId = H5D.create(GroupId, Hdf5Utils.NormalizedName(Datasetname), _datatype, _spaceId, H5P.DEFAULT, _propId);
/* Write data to dataset */
GCHandle hnd = GCHandle.Alloc(dataset, GCHandleType.Pinned);
_status = H5D.write(_datasetId, _datatype, H5S.ALL, H5S.ALL, H5P.DEFAULT,
hnd.AddrOfPinnedObject());
hnd.Free();
H5S.close(_spaceId);
_spaceId = -1;
}
else
{
AppendDataset(dataset);
}
}
// 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 static int WriteAsciiString(long groupId, string name, string str)
{
var spaceNullId = H5S.create(H5S.class_t.NULL);
var spaceScalarId = H5S.create(H5S.class_t.SCALAR);
// create two datasets of the extended ASCII character set
// store as H5T.FORTRAN_S1 -> space padding
int strLength = str.Length;
ulong[] dims = { (ulong)strLength, 1 };
/* Create the dataset. */
//name = ToHdf5Name(name);
var spaceId = H5S.create_simple(1, dims, null);
var datasetId = H5D.create(groupId, Hdf5Utils.NormalizedName(name), H5T.FORTRAN_S1, spaceId);
H5S.close(spaceId);
// we write from C and must provide null-terminated strings
byte[] wdata = new byte[strLength * 2];
//for (int i = 0; i < strLength; ++i)
//{
// wdata[2 * i] = (byte)i;
//}
for (int i = 0; i < strLength; ++i)
{
wdata[2 * i] = Convert.ToByte(str[i]);
}
var memId = H5T.copy(H5T.C_S1);
H5T.set_size(memId, new IntPtr(2));
//H5T.set_strpad(memId, H5T.str_t.NULLTERM);
GCHandle hnd = GCHandle.Alloc(wdata, GCHandleType.Pinned);
int result = H5D.write(datasetId, memId, H5S.ALL,
H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
H5T.close(memId);
H5D.close(datasetId);
return(result);
}
public void FirstDataset(Array dataset)
{
if (GroupId <= 0)
{
throw new Hdf5Exception("cannot call FirstDataset because group or file couldn't be created");
}
if (Hdf5Utils.GetRealName(GroupId, Datasetname, string.Empty).valid)
{
throw new Hdf5Exception("cannot call FirstDataset because dataset already exists");
}
Rank = dataset.Rank;
_currentDims = GetDims(dataset);
/* Create the data space with unlimited dimensions. */
_spaceId = H5S.create_simple(Rank, _currentDims, _maxDims);
/* Modify dataset creation properties, i.e. enable chunking */
_propId = H5P.create(H5P.DATASET_CREATE);
_status = H5P.set_chunk(_propId, Rank, _chunkDims);
/* Create a new dataset within the file using chunk creation properties. */
_datasetId = H5D.create(GroupId, Hdf5Utils.NormalizedName(Datasetname), _datatype, _spaceId, H5P.DEFAULT, _propId);
/* Write data to dataset */
GCHandle hnd = GCHandle.Alloc(dataset, GCHandleType.Pinned);
_status = H5D.write(_datasetId, _datatype, H5S.ALL, H5S.ALL, H5P.DEFAULT,
hnd.AddrOfPinnedObject());
if (_status < 0)
{
Hdf5Utils.LogError("Unable to write dataset");
}
hnd.Free();
H5S.close(_spaceId);
_spaceId = -1;
}
public static string ReadAsciiString(long groupId, string name)
{
var datatype = H5T.FORTRAN_S1;
//name = ToHdf5Name(name);
var datasetId = H5D.open(groupId, Hdf5Utils.NormalizedName(name));
var spaceId = H5D.get_space(datasetId);
int rank = H5S.get_simple_extent_ndims(spaceId);
ulong[] maxDims = new ulong[rank];
ulong[] dims = new ulong[rank];
ulong[] chunkDims = new ulong[rank];
var memId_n = H5S.get_simple_extent_dims(spaceId, dims, null);
// we write from C and must provide null-terminated strings
byte[] wdata = new byte[dims[0] * 2];
var memId = H5T.copy(H5T.C_S1);
H5T.set_size(memId, new IntPtr(2));
//H5T.set_strpad(memId, H5T.str_t.NULLTERM);
GCHandle hnd = GCHandle.Alloc(wdata, GCHandleType.Pinned);
int resultId = H5D.read(datasetId, memId, H5S.ALL,
H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
wdata = wdata.Where((b, i) => i % 2 == 0).
Select(b => (b == 0) ? (byte)32 : b).ToArray();
string result = Encoding.ASCII.GetString(wdata);
H5T.close(memId);
H5D.close(datasetId);
return(result);
}
public static int WriteUnicodeString(long groupId, string name, string str, H5T.str_t strPad = H5T.str_t.SPACEPAD)
{
byte[] wdata = Encoding.UTF8.GetBytes(str);
long spaceId = H5S.create(H5S.class_t.SCALAR);
long dtype = H5T.create(H5T.class_t.NO_CLASS, new IntPtr(wdata.Length));
H5T.set_cset(dtype, H5T.cset_t.UTF8);
H5T.set_strpad(dtype, strPad);
long datasetId = H5D.create(groupId, Hdf5Utils.NormalizedName(name), dtype, spaceId);
GCHandle hnd = GCHandle.Alloc(wdata, GCHandleType.Pinned);
int result = H5D.write(datasetId, dtype, H5S.ALL,
H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
H5T.close(dtype);
H5D.close(datasetId);
H5S.close(spaceId);
return(result);
}
public static T ReadObject <T>(long groupId, T readValue, string groupName)
{
if (readValue == null)
{
throw new ArgumentNullException(nameof(readValue));
}
Type tyObject = readValue.GetType();
//foreach (Attribute attr in Attribute.GetCustomAttributes(tyObject))
//{
// if (attr is Hdf5GroupName)
// groupName = (attr as Hdf5GroupName).Name;
// if (attr is Hdf5SaveAttribute)
// {
// Hdf5SaveAttribute atLeg = attr as Hdf5SaveAttribute;
// if (atLeg.SaveKind == Hdf5Save.DoNotSave)
// return readValue;
// }
//}
bool isGroupName = !string.IsNullOrWhiteSpace(groupName);
if (isGroupName)
{
groupId = H5G.open(groupId, Hdf5Utils.NormalizedName(groupName));
}
ReadFields(tyObject, readValue, groupId);
ReadProperties(tyObject, readValue, groupId);
if (isGroupName)
{
CloseGroup(groupId);
}
return(readValue);
}
public static string ReadUnicodeString(long groupId, string name)
{
var datasetId = H5D.open(groupId, Hdf5Utils.NormalizedName(name));
var typeId = H5D.get_type(datasetId);
if (H5T.is_variable_str(typeId) > 0)
{
var spaceId = H5D.get_space(datasetId);
long count = H5S.get_simple_extent_npoints(spaceId);
IntPtr[] rdata = new IntPtr[count];
GCHandle hnd = GCHandle.Alloc(rdata, GCHandleType.Pinned);
H5D.read(datasetId, typeId, H5S.ALL, H5S.ALL,
H5P.DEFAULT, hnd.AddrOfPinnedObject());
var attrStrings = new List <string>();
for (int i = 0; i < rdata.Length; ++i)
{
int attrLength = 0;
while (Marshal.ReadByte(rdata[i], attrLength) != 0)
{
++attrLength;
}
byte[] buffer = new byte[attrLength];
Marshal.Copy(rdata[i], buffer, 0, buffer.Length);
string stringPart = Encoding.UTF8.GetString(buffer);
attrStrings.Add(stringPart);
H5.free_memory(rdata[i]);
}
hnd.Free();
H5S.close(spaceId);
H5D.close(datasetId);
return(attrStrings[0]);
}
// Must be a non-variable length string.
int size = H5T.get_size(typeId).ToInt32();
IntPtr iPtr = Marshal.AllocHGlobal(size);
int result = H5D.read(datasetId, typeId, H5S.ALL, H5S.ALL,
H5P.DEFAULT, iPtr);
if (result < 0)
{
throw new IOException("Failed to read dataset");
}
var strDest = new byte[size];
Marshal.Copy(iPtr, strDest, 0, size);
Marshal.FreeHGlobal(iPtr);
H5D.close(datasetId);
return(Encoding.UTF8.GetString(strDest).TrimEnd((char)0));
}
public static long CreateOrOpenGroup(long groupId, string groupName)
{
return((Hdf5Utils.ItemExists(groupId, groupName, Hdf5ElementType.Group))
? H5G.open(groupId, Hdf5Utils.NormalizedName(groupName))
: H5G.create(groupId, Hdf5Utils.NormalizedName(groupName)));
}