public static IEnumerable <OffsetInfo> GetCompoundInfo(Type type, bool ieee = false)
{
//Type t = typeof(T);
var strtype = H5T.copy(H5T.C_S1);
int strsize = (int)H5T.get_size(strtype);
int curSize = 0;
List <OffsetInfo> offsets = new List <OffsetInfo>();
foreach (var x in type.GetFields())
{
OffsetInfo oi = new OffsetInfo()
{
name = x.Name,
type = x.FieldType,
datatype = ieee ? GetDatatypeIEEE(x.FieldType) : GetDatatype(x.FieldType),
size = x.FieldType == typeof(string) ? stringLength(x) : Marshal.SizeOf(x.FieldType),
offset = 0 + curSize
};
if (oi.datatype == H5T.C_S1)
{
strtype = H5T.copy(H5T.C_S1);
H5T.set_size(strtype, new IntPtr(oi.size));
oi.datatype = strtype;
}
if (oi.datatype == H5T.STD_I64BE)
{
oi.size = oi.size * 2;
}
curSize = curSize + oi.size;
offsets.Add(oi);
}
H5T.close(strtype);
return(offsets);
}
public static int WriteDatasetFromArray <T>(hid_t groupId, string name, Array dset, string datasetName = null) //where T : struct
{
int rank = dset.Rank;
ulong[] dims = Enumerable.Range(0, rank).Select(i => { return((ulong)dset.GetLength(i)); }).ToArray();
ulong[] maxDims = null;
var spaceId = H5S.create_simple(rank, dims, maxDims);
var datatype = GetDatatype(typeof(T));
var typeId = H5T.copy(datatype);
if (datatype == H5T.C_S1)
{
H5T.set_size(datatype, new IntPtr(2));
}
var datasetId = H5D.create(groupId, name, datatype, spaceId);
GCHandle hnd = GCHandle.Alloc(dset, GCHandleType.Pinned);
var result = H5D.write(datasetId, datatype, H5S.ALL, H5S.ALL, H5P.DEFAULT,
hnd.AddrOfPinnedObject());
hnd.Free();
H5D.close(datasetId);
H5S.close(spaceId);
H5T.close(typeId);
return(result);
}
public static unsafe void AddDataWithSharedDataType(long fileId, ContainerType container)
{
long typeId = H5T.copy(H5T.C_S1);
H5T.set_size(typeId, H5T.VARIABLE);
H5T.set_cset(typeId, H5T.cset_t.UTF8);
H5T.commit(fileId, "string_t", typeId);
var data = new string[] { "001", "11", "22", "33", "44", "55", "66", "77", " ", "AA", "ZZ", "!!" };
var dataChar = data
.SelectMany(value => Encoding.ASCII.GetBytes(value + '\0'))
.ToArray();
fixed(byte *dataVarPtr = dataChar)
{
var basePtr = new IntPtr(dataVarPtr);
var addresses = new IntPtr[]
{
IntPtr.Add(basePtr, 0), IntPtr.Add(basePtr, 4), IntPtr.Add(basePtr, 7), IntPtr.Add(basePtr, 10),
IntPtr.Add(basePtr, 13), IntPtr.Add(basePtr, 16), IntPtr.Add(basePtr, 19), IntPtr.Add(basePtr, 22),
IntPtr.Add(basePtr, 25), IntPtr.Add(basePtr, 28), IntPtr.Add(basePtr, 31), IntPtr.Add(basePtr, 34)
};
fixed(void *dataVarAddressesPtr = addresses)
{
TestUtils.Add(container, fileId, "shared_data_type", "shared_data_type", typeId, dataVarAddressesPtr, length: 12);
}
}
if (H5I.is_valid(typeId) > 0)
{
H5T.close(typeId);
}
}
public static double[, ,] ReadFieldData3D(string fileName)
{
H5FileId fileId = H5F.open(fileName, H5F.OpenMode.ACC_RDONLY);
H5DataSetId fDataSetId = H5D.open(fileId, "/FieldData/FD/f0");
H5DataTypeId fDataTypeId = H5D.getType(fDataSetId);
if (!H5T.equal(fDataTypeId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
{
Console.WriteLine("Error: Invalid dataset type, expected {0}", H5T.H5Type.NATIVE_FLOAT);
}
long[] dims = H5S.getSimpleExtentDims(H5D.getSpace(fDataSetId)).ToArray();
if (dims.Length != 3)
{
Console.WriteLine("Error: Invalid field data dimensions");
}
float[, ,] data = new float[dims[0], dims[1], dims[2]];
H5D.read(fDataSetId, fDataTypeId, new H5Array <float>(data));
// Reorder
double[, ,] fieldValues = new double[dims[2], dims[1], dims[0]];
for (int i = 0; i < dims[0]; i++)
{
for (int j = 0; j < dims[1]; j++)
{
for (int k = 0; k < dims[2]; k++)
{
fieldValues[k, j, i] = data[i, j, k];
}
}
}
return(fieldValues);
}
public static double[][] ReadMesh(string fileName)
{
double[][] meshes = new double[3][];
string[] meshNames = { "x", "y", "z" };
H5FileId fileId = H5F.open(fileName, H5F.OpenMode.ACC_RDONLY);
for (int i = 0; i < meshNames.Length; i++)
{
H5DataSetId dsId = H5D.open(fileId, "/Mesh/" + meshNames[i]);
H5DataTypeId dtId = H5D.getType(dsId);
if (!H5T.equal(dtId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
{
Console.WriteLine("Error: Invalid dataset type, expected {0}", H5T.H5Type.NATIVE_FLOAT);
}
float[] mesh = new float[H5D.getStorageSize(dsId) / H5T.getSize(dtId)];
H5D.read(dsId, dtId, new H5Array <float>(mesh));
meshes[i] = mesh.Select(x => (double)x * 1000.0).ToArray(); // m -> mm
H5D.close(dsId);
H5T.close(dtId);
}
H5F.close(fileId);
return(meshes);
}
public static int WritePrimitiveAttribute <T>(hid_t groupId, string name, Array attributes, string datasetName = null) //where T : struct
{
var tmpId = groupId;
if (!string.IsNullOrWhiteSpace(datasetName))
{
var datasetId = H5D.open(groupId, datasetName);
if (datasetId > 0)
{
groupId = datasetId;
}
}
int rank = attributes.Rank;
ulong[] dims = Enumerable.Range(0, rank).Select(i =>
{ return((ulong)attributes.GetLength(i)); }).ToArray();
ulong[] maxDims = null;
var spaceId = H5S.create_simple(rank, dims, maxDims);
var datatype = GetDatatype(typeof(T));
var typeId = H5T.copy(datatype);
var attributeId = H5A.create(groupId, name, datatype, spaceId);
GCHandle hnd = GCHandle.Alloc(attributes, GCHandleType.Pinned);
var result = H5A.write(attributeId, datatype, hnd.AddrOfPinnedObject());
hnd.Free();
H5A.close(attributeId);
H5S.close(spaceId);
H5T.close(typeId);
if (tmpId != groupId)
{
H5D.close(groupId);
}
return(result);
}
public static double ReadAttribute(string file, string dataSetOrGroup, string attribute)
{
double attr = Double.NaN;
try
{
H5FileId fileId = H5F.open(file, H5F.OpenMode.ACC_RDONLY);
H5ObjectInfo objectInfo = H5O.getInfoByName(fileId, dataSetOrGroup);
H5GroupId groupId = null;
H5DataSetId dataSetId = null;
H5AttributeId attrId;
if (objectInfo.objectType == H5ObjectType.GROUP)
{
groupId = H5G.open(fileId, dataSetOrGroup);
attrId = H5A.open(groupId, attribute);
}
else
{
dataSetId = H5D.open(fileId, dataSetOrGroup);
attrId = H5A.open(dataSetId, attribute);
}
H5DataTypeId attrTypeId = H5A.getType(attrId);
double[] dAttrs = new double[] { };
if (H5T.equal(attrTypeId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
{
float[] fAttrs = new float[H5S.getSimpleExtentNPoints(H5A.getSpace(attrId))];
H5A.read(attrId, attrTypeId, new H5Array <float>(fAttrs));
dAttrs = (from f in fAttrs select(double) f).ToArray();
}
else if (H5T.equal(attrTypeId, H5T.copy(H5T.H5Type.NATIVE_DOUBLE)))
{
dAttrs = new double[H5S.getSimpleExtentNPoints(H5A.getSpace(attrId))];
H5A.read(attrId, attrTypeId, new H5Array <double>(dAttrs));
}
H5T.close(attrTypeId);
H5A.close(attrId);
if (groupId != null)
{
H5G.close(groupId);
}
if (dataSetId != null)
{
H5D.close(dataSetId);
}
H5F.close(fileId);
return((double)dAttrs[0]);
}
catch (HDFException e)
{
Console.WriteLine("Error: Unhandled HDF5 exception");
Console.WriteLine(e.Message);
}
return(attr);
}
public void H5DreadTest1()
{
byte[] rdata = new byte[512];
hid_t mem_type = H5T.copy(H5T.C_S1);
Assert.IsTrue(H5T.set_size(mem_type, new IntPtr(2)) >= 0);
GCHandle hnd = GCHandle.Alloc(rdata, GCHandleType.Pinned);
Assert.IsTrue(H5D.read(m_v0_ascii_dset, mem_type, H5S.ALL,
H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject()) >= 0);
for (int i = 0; i < 256; ++i)
{
// H5T.FORTRAN_S1 is space (= ASCII dec. 32) padded
if (i != 32)
{
Assert.IsTrue(rdata[2 * i] == (byte)i);
}
else
{
Assert.IsTrue(rdata[64] == (byte)0);
}
Assert.IsTrue(rdata[2 * i + 1] == (byte)0);
}
hnd.Free();
Assert.IsTrue(H5T.close(mem_type) >= 0);
}
public static void Write1DArray <T>(Hdf5Dataset _dataset, T[] _array)
{
if (_dataset.Dataspace.NumberOfDimensions != 1)
{
throw new Hdf5ArrayDimensionsMismatchException();
}
if ((ulong)_array.Length != _dataset.Dataspace.DimensionProperties[0].CurrentSize)
{
throw new Hdf5ArraySizeMismatchException();
}
var datasetId = H5O.open(_dataset.FileId.Value, _dataset.Path.FullPath).ToId();
GCHandle arrayHandle = GCHandle.Alloc(_array, GCHandleType.Pinned);
var typeId = H5T.copy(_dataset.DataType.NativeType.Value).ToId();
int result = H5D.write(
datasetId.Value,
typeId.Value,
H5S.ALL,
H5S.ALL,
H5P.DEFAULT,
arrayHandle.AddrOfPinnedObject());
arrayHandle.Free();
H5T.close(typeId.Value);
H5O.close(datasetId.Value);
FileHelper.FlushToFile(_dataset.FileId);
}
private bool setOMXFileAttributes()
{
// write OMX attributes
H5DataSpaceId dspace;
H5DataTypeId dtype;
H5AttributeId attr;
// OMX version
dspace = H5S.create(H5S.H5SClass.SCALAR);
dtype = H5T.copy(H5T.H5Type.C_S1); // string datatype
H5T.setSize(dtype, dllVersion[0].Length);
attr = H5A.create(fileId, omxVersionName, dtype, dspace);
ASCIIEncoding ascii = new ASCIIEncoding();
H5A.write(attr, dtype, new H5Array <System.Byte>(ascii.GetBytes(dllVersion[0])));
H5A.close(attr);
// OMX shape - only 2D tables
dspace = H5S.create_simple(1, new long[] { 2 });
dtype = H5T.copy(H5T.H5Type.NATIVE_INT);
attr = H5A.create(fileId, omxShapeAttr, dtype, dspace);
int[] shape = new int[2];
shape[0] = (int)Shape[0];
shape[1] = (int)Shape[1];
H5A.write <int>(attr, dtype, new H5Array <int>(shape));
H5S.close(dspace);
H5A.close(attr);
return(true);
}
// test that we can create an empty file and add matrices
public static void CreateMatrixTest(string file)
{
int zones = 3;
double[,] testblock;
string[] matrixNames = { "mat1", "mat2" };
OmxWriteStream ws = OmxFile.Create(file, zones, true);
// NOTE: cannot create data type until after file stream is created
H5DataTypeId matrixDataTypes = H5T.copy(H5T.H5Type.NATIVE_DOUBLE);
for (int i = 0; i < matrixNames.Length; i++)
{
ws.AddMatrix(matrixNames[i], matrixDataTypes);
}
ws.Close();
OmxReadStream rs = OmxFile.OpenReadOnly(file);
for (int i = 0; i < matrixNames.Length; i++)
{
testblock = rs.GetMatrixBlock <double>(matrixNames[i], 0, 0, 1, 1);
}
Console.WriteLine("mat shape is {0},{1}", rs.Shape[0], rs.Shape[1]);
Console.WriteLine("mat names are {0},{1}", rs.MatrixNames[0], rs.MatrixNames[1]);
Console.WriteLine("mat data type: {0},{1}",
H5T.getClass(rs.GetMatrixDataType(matrixNames[0])),
H5T.getClass(rs.GetMatrixDataType(matrixNames[1])));
rs.Close();
}
public void H5TcloseTest1()
{
hid_t dtype = H5T.copy(H5T.IEEE_F64LE);
Assert.IsTrue(dtype >= 0);
Assert.IsTrue(H5T.close(dtype) >= 0);
}
/// <summary>
/// 写数据集属性
/// </summary>
public void WriteDatasetAttribute(string datasetName, string attrName, string value)
{
H5DataSetId datasetId = H5D.open(_fileId, datasetName);
H5DataTypeId typeId = H5T.copy(H5T.H5Type.C_S1);
H5DataSpaceId spaceId = H5S.create(H5S.H5SClass.SCALAR);
H5T.setSize(typeId, value.Length);
H5AttributeId attrId = H5A.create(datasetId, attrName, typeId, spaceId);
if (value != "")
{
H5Array <byte> buffer = new H5Array <byte>(Encoding.Default.GetBytes(value));
H5A.write(attrId, typeId, buffer);
}
if (typeId != null)
{
H5T.close(typeId);
}
if (spaceId != null)
{
H5S.close(spaceId);
}
if (attrId != null)
{
H5A.close(attrId);
}
if (datasetId != null)
{
H5D.close(datasetId);
}
}
public static long OpenHDFDataType(Type clrType, long maxSize = 1)
{
if (clrType == typeof(double))
{
return(H5T.copy(H5T.NATIVE_DOUBLE));
}
if (clrType == typeof(float))
{
return(H5T.copy(H5T.NATIVE_FLOAT));
}
if (clrType == typeof(int))
{
return(H5T.copy(H5T.NATIVE_INT32));
}
if (clrType == typeof(long))
{
return(H5T.copy(H5T.NATIVE_INT64));
}
if (clrType == typeof(string))
{
var type = H5T.copy(H5T.C_S1);
var ptr = new IntPtr(maxSize);//Leak?
var status = H5T.set_size(type, ptr);
Debug.Assert(status >= 0);
return(type);
}
throw new NotImplementedException();
}
public static int WriteDataset <T>(int groupId, string name, T[,] dset) where T : struct
{
ulong[] dims = new ulong[] { (ulong)dset.GetLength(0), (ulong)dset.GetLength(1) };
ulong[] maxDims = null;
var spaceId = H5S.create_simple(2, dims, maxDims);
var datatype = GetDatatype(typeof(T));
var typeId = H5T.copy(datatype);
if (datatype == H5T.C_S1)
{
H5T.set_size(datatype, new IntPtr(2));
//var wdata = Encoding.ASCII.GetBytes((char[,]) dset);
}
name = ToHdf5Name(name);
var datasetId = H5D.create(groupId, name, datatype, spaceId);
GCHandle hnd = GCHandle.Alloc(dset, GCHandleType.Pinned);
var result = H5D.write(datasetId, datatype, H5S.ALL, H5S.ALL, H5P.DEFAULT,
hnd.AddrOfPinnedObject());
hnd.Free();
H5D.close(datasetId);
H5S.close(spaceId);
H5T.close(typeId);
return(result);
}
private static double[,] ReadDataArray(hid_t fileLoc, string name, bool transpose = false)
{
hid_t dset = H5D.open(fileLoc, name);
hid_t fspace = H5D.get_space(dset);
hid_t count = H5S.get_simple_extent_ndims(fspace);
hid_t type = H5D.get_type(dset);
hsize_t[] dims = new hsize_t[count];
hsize_t[] maxdims = new hsize_t[count];
H5S.get_simple_extent_dims(fspace, dims, maxdims);
H5S.close(fspace);
byte[] rdata = new byte[dims[0] * dims[1] * 8];
hid_t mem_type = H5T.copy(H5T.NATIVE_DOUBLE);
H5T.set_size(mem_type, new IntPtr(8));
GCHandle hnd = GCHandle.Alloc(rdata, GCHandleType.Pinned);
H5D.read(dset, mem_type, H5S.ALL,
H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
H5T.close(mem_type);
if (transpose)
{
double[,] val = new double[dims[1], dims[0]];
int cnt = 0;
for (int i = 0; i < (int)dims[0]; i++)
{
for (int j = 0; j < (int)dims[1]; j++)
{
val[j, i] = BitConverter.ToDouble(rdata, cnt * 8);
cnt++;
}
}
return(val);
}
else
{
double[,] val = new double[dims[0], dims[1]];
int cnt = 0;
for (int i = 0; i < (int)dims[0]; i++)
{
for (int j = 0; j < (int)dims[1]; j++)
{
val[i, j] = BitConverter.ToDouble(rdata, cnt * 8);
cnt++;
}
}
return(val);
}
}
private static void WriteFile(string filePath)
{
var file = H5F.create(filePath, H5F.CreateMode.ACC_TRUNC);
var group = H5G.create(file, "/group");
H5G.close(group);
const int RANK = 2;
const int DIM0 = 3;
const int DIM1 = 4;
var dims = new long[RANK] {
DIM0, DIM1
};
var dataSpace = H5S.create_simple(RANK, dims);
var dataSet = H5D.create(file, "/group/dataset", H5T.H5Type.NATIVE_INT, dataSpace);
H5S.close(dataSpace);
var data = new int[DIM0, DIM1]
{
{ 1, 2, 3, 4 },
{ 5, 6, 7, 8 },
{ 9, 10, 11, 12 }
};
H5D.write(dataSet, new H5DataTypeId(H5T.H5Type.NATIVE_INT), new H5Array <int>(data));
var dataType = new H5DataTypeId(H5T.H5Type.NATIVE_INT);
dataSpace = H5S.create(H5S.H5SClass.SCALAR);
var integerAttribute = H5A.create(dataSet, "int", dataType, dataSpace);
H5A.write(integerAttribute, dataType, new H5Array <int>(new int[1] {
42
}));
H5A.close(integerAttribute);
H5S.close(dataSpace);
//H5T.close(dataType); // Read-only.
var str = "Hello, world!";
var strBytes = Encoding.ASCII.GetBytes(str);
// There is a H5T.get_cset, but there does not seem to be a way of setting the character encoding, i.e. set_cset.
dataType = H5T.copy(H5T.H5Type.C_S1);
H5T.setSize(dataType, strBytes.Length);
dataSpace = H5S.create(H5S.H5SClass.SCALAR);
var stringAttribute = H5A.create(dataSet, "string", dataType, dataSpace);
H5A.write(stringAttribute, dataType, new H5Array <byte>(strBytes));
H5A.close(stringAttribute);
H5S.close(dataSpace);
H5T.close(dataType);
H5D.close(dataSet);
H5F.close(file);
}
/// <summary>
/// Constructor to create a chuncked dataset object
/// </summary>
/// <param name="name"></param>
/// <param name="groupId"></param>
public ChunkedDataset(string name, long groupId)
{
Datasetname = name;
GroupId = groupId;
datatype = Hdf5.GetDatatype(typeof(T));
typeId = H5T.copy(datatype);
chunkDims = null;
}
/// <summary>
/// Constructor to create a chuncked dataset object
/// </summary>
/// <param name="name"></param>
/// <param name="groupId"></param>
/// <param name="chunkSize"></param>
public ChunkedDataset(string name, long groupId, ulong[] chunkSize)
{
Datasetname = name;
GroupId = groupId;
_datatype = Hdf5.GetDatatype(typeof(T));
_typeId = H5T.copy(_datatype);
_chunkDims = chunkSize;
}
public static Hdf5Dataset CreateDataset(
Hdf5Identifier _fileId,
Hdf5Path _parentPath,
string _name,
Hdf5DataTypes _datatype,
int _numberOfDimensions,
List <Hdf5DimensionProperty> _properties)
{
Hdf5Path path = _parentPath.Append(_name);
UInt64[] dimensionSize = new UInt64[_numberOfDimensions];
UInt64[] maxSize = null; // new UInt64[_numberOfDimensions];
int i = 0;
foreach (var property in _properties)
{
dimensionSize[i] = property.CurrentSize;
//if (property.MaximumSize == UInt64.MaxValue)
//{
// maxSize[i] = H5S.UNLIMITED;
//}
//else
//{
// maxSize[i] = property.MaximumSize;
//}
i++;
}
Hdf5Identifier dataspaceId = H5S.create_simple(_numberOfDimensions, dimensionSize, maxSize).ToId();
//TODO handle string datasets
Hdf5Identifier typeId = H5T.copy(TypeHelper.GetNativeType(_datatype).Value).ToId();
var status = H5T.set_order(typeId.Value, H5T.order_t.LE);
Hdf5Identifier datasetId = H5D.create(_fileId.Value, path.FullPath, typeId.Value, dataspaceId.Value).ToId();
Hdf5Dataset dataset = null;
if (datasetId.Value > 0)
{
dataset = new Hdf5Dataset(_fileId, datasetId, path.FullPath)
{
DataType = TypeHelper.GetDataTypeFromDataset(datasetId),
Dataspace = DataspaceHelper.GetDataspace(datasetId)
};
H5D.close(datasetId.Value);
}
H5T.close(typeId.Value);
FileHelper.FlushToFile(_fileId);
return(dataset);
}
public static unsafe void AddString(long fileId, ContainerType container)
{
long res;
var dims = new ulong[] { 2, 2, 3 }; /* "extendible contiguous non-external dataset not allowed" */
// fixed length string attribute (ASCII)
var typeIdFixed = H5T.copy(H5T.C_S1);
res = H5T.set_size(typeIdFixed, new IntPtr(2));
res = H5T.set_cset(typeIdFixed, H5T.cset_t.ASCII);
var dataFixed = new string[] { "00", "11", "22", "33", "44", "55", "66", "77", " ", "AA", "ZZ", "!!" };
var dataFixedChar = dataFixed
.SelectMany(value => Encoding.ASCII.GetBytes(value))
.ToArray();
TestUtils.Add(container, fileId, "string", "fixed", typeIdFixed, dataFixedChar.AsSpan(), dims);
res = H5T.close(typeIdFixed);
// variable length string attribute (ASCII)
var typeIdVar = H5T.copy(H5T.C_S1);
res = H5T.set_size(typeIdVar, H5T.VARIABLE);
res = H5T.set_cset(typeIdVar, H5T.cset_t.ASCII);
var dataVar = new string[] { "00", "11", "22", "33", "44", "55", "66", "77", " ", "AA", "ZZ", "!!" };
var dataVarIntPtr = dataVar.Select(x => Marshal.StringToCoTaskMemUTF8(x)).ToArray();
TestUtils.Add(container, fileId, "string", "variable", typeIdVar, dataVarIntPtr.AsSpan(), dims);
foreach (var ptr in dataVarIntPtr)
{
Marshal.FreeCoTaskMem(ptr);
}
res = H5T.close(typeIdVar);
// variable length string attribute (UTF8)
var typeIdVarUTF8 = H5T.copy(H5T.C_S1);
res = H5T.set_size(typeIdVarUTF8, H5T.VARIABLE);
res = H5T.set_cset(typeIdVarUTF8, H5T.cset_t.UTF8);
var dataVarUTF8 = new string[] { "00", "11", "22", "33", "44", "55", "66", "77", " ", "ÄÄ", "的的", "!!" };
var dataVarUTF8IntPtr = dataVarUTF8.Select(x => Marshal.StringToCoTaskMemUTF8(x)).ToArray();
TestUtils.Add(container, fileId, "string", "variableUTF8", typeIdVarUTF8, dataVarUTF8IntPtr.AsSpan(), dims);
foreach (var ptr in dataVarUTF8IntPtr)
{
Marshal.FreeCoTaskMem(ptr);
}
res = H5T.close(typeIdVarUTF8);
}
public static int AttributeAsInt32(H5AttributeId _attributeId)
{
H5DataTypeId attributeType = H5T.copy(H5T.H5Type.NATIVE_INT);
int[] value = new int[1];
H5A.read <int>(_attributeId, attributeType, new H5Array <int>(value));
return(value[0]);
}
public static Double AttributeAsDouble(H5AttributeId _attributeId)
{
H5DataTypeId attributeType = H5T.copy(H5T.H5Type.NATIVE_DOUBLE);
double[] value = new double[1];
H5A.read <double>(_attributeId, attributeType, new H5Array <double>(value));
return(value[0]);
}
/// <summary>
/// Constructor to create a chuncked dataset object
/// </summary>
/// <param name="name"></param>
/// <param name="groupId"></param>
/// <param name="chunckSize"></param>
public ChunkedDataset(string name, hid_t groupId, ulong[] chunckSize)
{
//Datasetname = Hdf5.ToHdf5Name(name);
Datasetname = name;
GroupId = groupId;
datatype = Hdf5.GetDatatype(typeof(T));
typeId = H5T.copy(datatype);
chunkDims = chunckSize;
}
private static byte[] EncodeStringData(string str, out H5DataTypeId dtype)
{
byte[] strdata = System.Text.Encoding.UTF8.GetBytes(str);
dtype = H5T.copy(H5T.H5Type.C_S1);
H5T.setSize(dtype, strdata.Length);
return(strdata);
}
// Generate floating number attributes
// GroupName: target group for the new attribute
// AttName: attribute name
// AttContent: content for the attribute, has to be a single floating number, here 32bit floating number is used, consider using 64bit double if necessary
public static void NumberAttributeGenerator(H5GroupId GroupName, string AttName, float AttContent)
{
float[] AttArray = new float[1] {
AttContent
};
long[] dims = new long[1];
dims[0] = AttArray.Length;
H5AttributeId attributeId = H5A.create(GroupName, AttName, H5T.copy(H5T.H5Type.NATIVE_FLOAT), H5S.create_simple(1, dims));
H5A.write(attributeId, H5T.copy(H5T.H5Type.NATIVE_FLOAT), new H5Array <float>(AttArray));
H5A.close(attributeId);
}
public void H5TcommitTest1()
{
hid_t dtype = H5T.copy(H5T.IEEE_F64LE);
Assert.IsTrue(dtype >= 0);
Assert.IsTrue(H5T.commit(m_v0_test_file, "foo", dtype) >= 0);
// can't commit twice
Assert.IsFalse(H5T.commit(m_v0_test_file, "bar", dtype) >= 0);
// can't commit to different files
Assert.IsFalse(H5T.commit(m_v2_test_file, "bar", dtype) >= 0);
Assert.IsTrue(H5T.close(dtype) >= 0);
}
// Generate double attributes
// GroupName: target group for the new attribute
// AttName: attribute name
// AttContent: content for the attribute, has to be a single floating number, here 64bit double is used, to generate subgroups in Data
public static void DoubleAttributeGenerator(H5GroupId GroupName, string AttName, double AttContent)
{
double[] AttArray = new double[1] {
AttContent
};
long[] dims = new long[1];
dims[0] = AttArray.Length;
H5AttributeId attributeId = H5A.create(GroupName, AttName, H5T.copy(H5T.H5Type.NATIVE_DOUBLE), H5S.create_simple(1, dims));
H5A.write(attributeId, H5T.copy(H5T.H5Type.NATIVE_FLOAT), new H5Array <double>(AttArray));
H5A.close(attributeId);
}
static void Main2222(string[] args)
{
var h5 = H5F.create(@"D:\test.h5", H5F.ACC_TRUNC);
var typeId = H5T.create(H5T.class_t.COMPOUND, new IntPtr(40));
var strtype = H5T.copy(H5T.C_S1);
H5T.set_size(strtype, new IntPtr(16));
H5T.insert(typeId, "Name", new IntPtr(0), strtype);
H5T.insert(typeId, "x_pos", new IntPtr(16), H5T.NATIVE_INT32);
H5T.insert(typeId, "y_pos", new IntPtr(20), H5T.NATIVE_INT32);
H5T.insert(typeId, "Mass", new IntPtr(24), H5T.NATIVE_FLOAT);
H5T.insert(typeId, "Temperature", new IntPtr(32), H5T.NATIVE_DOUBLE);
ulong[] dims = new ulong[] { 10000 };
ulong[] chunk_size = new ulong[] { 1000 };
var spaceid = H5S.create_simple(dims.Length, dims, null);
var dcpl = H5P.create(H5P.DATASET_CREATE);
H5P.set_layout(dcpl, H5D.layout_t.COMPACT);
H5P.set_deflate(dcpl, 6);
H5P.set_chunk(dcpl, chunk_size.Length, chunk_size);
var datasetid = H5D.create(h5, "Table1", typeId, spaceid, H5P.DEFAULT, dcpl);
ComType ct = new ComType()
{
Name = "aabb",
x_pos = 2,
y_pos = 1,
Mass = 1.24F,
Temperature = 45.7,
};
IntPtr p = Marshal.AllocHGlobal(40 * (int)dims[0]);
Marshal.StructureToPtr(ct, p, false);
H5D.write(datasetid, typeId, spaceid, H5S.ALL, H5P.DEFAULT, p);
H5F.close(h5);
}
private static void WriteAttribute(H5ObjectWithAttributes target, string name, long value)
{
H5DataTypeId dtype = H5T.copy(H5T.H5Type.NATIVE_LLONG);
H5DataSpaceId spaceId = H5S.create(H5S.H5SClass.SCALAR);
H5AttributeId attributeId = H5A.create(target, name, dtype, spaceId);
H5A.write(attributeId, dtype, new H5Array <long>(new[] { value }));
H5A.close(attributeId);
H5T.close(dtype);
H5S.close(spaceId);
}