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);
}
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 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 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 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 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);
}
}
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);
}
}
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);
}
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);
}
/// <summary>
/// Reads an n-dimensional dataset.
/// </summary>
/// <typeparam name="T">Generic parameter strings or primitive type</typeparam>
/// <param name="groupId">id of the group. Can also be a file Id</param>
/// <param name="name">name of the dataset</param>
/// <returns>The n-dimensional dataset</returns>
public static Array ReadDatasetToArray <T>(hid_t groupId, string name) //where T : struct
{
var datatype = GetDatatype(typeof(T));
var datasetId = H5D.open(groupId, name);
var spaceId = H5D.get_space(datasetId);
int rank = H5S.get_simple_extent_ndims(spaceId);
long count = H5S.get_simple_extent_npoints(spaceId);
Array dset;
Type type = typeof(T);
if (rank >= 0 && count >= 0)
{
int rankChunk;
ulong[] maxDims = new ulong[rank];
ulong[] dims = new ulong[rank];
ulong[] chunkDims = new ulong[rank];
hid_t memId = H5S.get_simple_extent_dims(spaceId, dims, maxDims);
long[] lengths = dims.Select(d => Convert.ToInt64(d)).ToArray();
dset = Array.CreateInstance(type, lengths);
var typeId = H5D.get_type(datasetId);
var mem_type = H5T.copy(datatype);
if (datatype == H5T.C_S1)
{
H5T.set_size(datatype, new IntPtr(2));
}
var propId = H5D.get_create_plist(datasetId);
if (H5D.layout_t.CHUNKED == H5P.get_layout(propId))
{
rankChunk = H5P.get_chunk(propId, rank, chunkDims);
}
memId = H5S.create_simple(rank, dims, maxDims);
GCHandle hnd = GCHandle.Alloc(dset, GCHandleType.Pinned);
H5D.read(datasetId, datatype, memId, spaceId,
H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
}
else
{
dset = Array.CreateInstance(type, new long[1] {
0
});
}
H5D.close(datasetId);
H5S.close(spaceId);
return(dset);
}
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));
}
long dcpl = H5P.DEFAULT;
if (datatype != H5T.C_S1)
{
Console.WriteLine("Do you want to compress the file? (Y/N)");
string response = "N";
response = Console.ReadLine();
if (response == "Y" || response == "y")
{
var cnt = dset.Length;
var log10 = (int)Math.Log10(cnt);
ulong pow = (ulong)Math.Pow(10, log10);
//ulong c_s = Math.Min(1000, pow);
ulong[] chunk_size = new ulong[] { pow };
//chunk_size[0] = ulong.Parse(Console.ReadLine());
Console.WriteLine("Auto-Chunking with chunk-size of {0} samples.", pow);
dcpl = create_property(chunk_size);
}
else
{
Console.WriteLine("Creating an Uncompressed File...");
}
}
var datasetId = H5D.create(groupId, name, datatype, spaceId, H5P.DEFAULT, dcpl);
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 hid_t AddDataString(hid_t parentLoc, string name, string data)
{
byte[][] wdata = new byte[1][];
wdata[0] = ASCIIEncoding.ASCII.GetBytes(data);
int n = wdata[0].Length + 1;
/*
* Create file and memory datatypes. For this example we will save
* the strings as FORTRAN strings, therefore they do not need space
* for the null terminator in the file.
*/
hsize_t[] dims = new hsize_t[1];
dims[0] = (hsize_t)1;
hid_t filetype = H5T.copy(H5T.FORTRAN_S1);
herr_t status = H5T.set_size(filetype, new IntPtr(n - 1));
hid_t memtype = H5T.copy(H5T.C_S1);
status = H5T.set_size(memtype, new IntPtr(n));
/*
* Create dataspace. Setting maximum size to NULL sets the maximum
* size to be the current size.
*/
hid_t space = H5S.create_simple(1, dims, null);
/*
* Create the dataset and write the string data to it.
*/
hid_t dset = H5D.create(parentLoc, name, filetype, space, H5P.DEFAULT, H5P.DEFAULT,
H5P.DEFAULT);
GCHandle hnd = GCHandle.Alloc(wdata[0], GCHandleType.Pinned);
// herr_t flag= H5D.write(dataSetId, type, H5S.ALL, H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject());
status = H5D.write(dset, memtype, H5S.ALL, H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject());
/*
* Close and release resources.
*/
status = H5D.close(dset);
status = H5S.close(space);
status = H5T.close(filetype);
status = H5T.close(memtype);
return(dset);
}
public static int WriteAsciiString(hid_t 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, 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);
}
private static string ReadDataCharArray(hid_t fileLoc, string name)
{
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]];
hid_t mem_type = H5T.copy(type);
H5T.set_size(mem_type, new IntPtr(1));
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);
char[] val = new char[dims[0]];
for (int i = 0; i < (int)dims[0]; i += 2)
{
val[i] = BitConverter.ToChar(rdata, i);
}
return(val.ToString());
}
public static T[,] ReadDataset <T>(int groupId, string name) where T : struct
{
var datatype = GetDatatype(typeof(T));
name = ToHdf5Name(name);
var datasetId = H5D.open(groupId, name);
var spaceId = H5D.get_space(datasetId);
int rank = H5S.get_simple_extent_ndims(spaceId);
long count = H5S.get_simple_extent_npoints(spaceId);
int rankChunk;
ulong[] maxDims = new ulong[rank];
ulong[] dims = new ulong[rank];
ulong[] chunkDims = new ulong[rank];
var memId = H5S.get_simple_extent_dims(spaceId, dims, maxDims);
T[,] dset = new T[dims[0], dims[1]];
var typeId = H5D.get_type(datasetId);
var mem_type = H5T.copy(datatype);
if (datatype == H5T.C_S1)
{
H5T.set_size(datatype, new IntPtr(2));
}
var propId = H5D.get_create_plist(datasetId);
if (H5D.layout_t.CHUNKED == H5P.get_layout(propId))
{
rankChunk = H5P.get_chunk(propId, rank, chunkDims);
}
memId = H5S.create_simple(rank, dims, maxDims);
GCHandle hnd = GCHandle.Alloc(dset, GCHandleType.Pinned);
H5D.read(datasetId, datatype, memId, spaceId,
H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
H5D.close(typeId);
H5D.close(datasetId);
H5S.close(spaceId);
return(dset);
}
private static hid_t CreateFixedStringType(byte[] bytes, bool utf8)
{
#if true
var type = H5T.create(H5T.class_t.STRING, new IntPtr(bytes.Length));
if (type < 0)
{
throw new Exception("Failed to create string type");
}
#else
var type = H5T.copy(H5T.C_S1);
if (type < 0)
{
throw new Exception("Failed to create string type");
}
// TODO: bytes.Length or bytes.Length + 1?
if (H5T.set_size(type, new IntPtr(bytes.Length)) < 0)
{
H5T.close(type);
throw new Exception("Failed to set type size");
}
#endif
if (utf8)
{
if (H5T.set_cset(type, H5T.cset_t.UTF8) < 0)
{
H5T.close(type);
throw new Exception("Failed to set cset");
}
}
if (H5T.set_strpad(type, H5T.str_t.NULLTERM) < 0)
{
H5T.close(type);
throw new Exception("Failed to set strpad");
}
return(type);
}
public static IEnumerable ReadStrings(string filename, string dataset)
{
var f = H5F.open(filename, H5F.ACC_RDONLY);
if (f < 0)
{
throw new Exception("Could not open file: " + filename);
}
var dset = H5D.open(f, Encoding.ASCII.GetBytes(dataset), H5P.DEFAULT);
if (dset < 0)
{
throw new Exception("Could not open dataset: " + dataset);
}
var filetype = H5D.get_type(dset);
var sdim = H5T.get_size(filetype) + 1;
var space = H5D.get_space(dset);
var ndims = H5S.get_simple_extent_ndims(space);
ulong[] dims = new ulong[ndims];
H5S.get_simple_extent_dims(space, dims, null);
var memtype = H5T.copy(H5T.C_S1);
var status = H5T.set_size(memtype, sdim);
int len = (int)(dims[0] * (ulong)sdim * SIZEOF_CHAR);
byte[] buffer = new byte[len];
IntPtr ptr = Marshal.AllocHGlobal(len);
status = H5D.read(dset, memtype, H5S.ALL, H5S.ALL, H5P.DEFAULT, ptr);
Marshal.Copy(ptr, buffer, 0, len);
Marshal.FreeHGlobal(ptr);
string s = Encoding.ASCII.GetString(buffer);
return(s.Split(new char[] { '\0' }, StringSplitOptions.RemoveEmptyEntries));
}
private static double ReadDataValue(hid_t fileLoc, string name)
{
hid_t dset = H5D.open(fileLoc, name);
byte[] rdata = new byte[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);
double val = BitConverter.ToDouble(rdata, 0);
return(val);
}
private static string ReadDataString(hid_t fileLoc, string name)
{
hid_t dset = H5D.open(fileLoc, name);
hid_t type = H5D.get_type(dset);
// H5T.is_variable_str(type);
IntPtr size = H5T.get_size(type);
hid_t fspace = H5D.get_space(dset);
hid_t mem_type = H5T.copy(type);
H5T.set_size(mem_type, size);
byte[] buffer = new byte[size.ToInt32()];
GCHandle hnd = GCHandle.Alloc(buffer, GCHandleType.Pinned);
H5D.read(dset, mem_type, H5S.ALL,
H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
H5T.close(mem_type);
// remove the last "/0"
if (buffer[buffer.Length - 1] == 0)
{
byte[] buffer2 = new byte[buffer.Length - 1];
for (int i = 0; i < buffer2.Length; i++)
{
buffer2[i] = buffer[i];
}
return(ASCIIEncoding.ASCII.GetString(buffer2));
}
return(ASCIIEncoding.ASCII.GetString(buffer));
}
//public static void WriteStringsToAscii(int groupId, string name, IEnumerable<string> strs)
//{
// var maxLength = strs.Select(s => s.Length).Max();
// ulong strSz = (ulong)strs.Count();
// var buf = strs.SelectMany(s => s.PadRight(maxLength).ToCharArray()).ToArray();
// ulong[] dimsa = new ulong[] { strSz, 1 };
// /* Create the data space for the dataset. */
// ulong[] dims = new ulong[] { strSz, (ulong)maxLength + 1 };
// var spaceId = H5S.create_simple(2, dims, null);
// /* Create the dataset. */
// name = ToHdf5Name(name);
// var datasetId = H5D.create(groupId, name, H5T.STD_I32BE, spaceId, H5P.DEFAULT);
// var aId = H5S.create_simple(2, dimsa, null);
// var aTypeId = H5T.copy(H5T.C_S1);
// H5T.set_size(aTypeId, new IntPtr(maxLength));
// var attr = H5A.create(datasetId, "string-att", aTypeId, aId, H5P.DEFAULT);
// GCHandle hnd = GCHandle.Alloc(buf, GCHandleType.Pinned);
// H5A.write(attr, aTypeId, hnd.AddrOfPinnedObject());
// hnd.Free();
// /* End access to the dataset and release resources used by it. */
// H5D.close(datasetId);
// /* Terminate access to the data space. */
// H5S.close(spaceId);
// H5S.close(aId);
// H5T.close(aTypeId);
// H5A.close(attr);
//}
public static int WriteStringsToAscii(int groupId, string name, IEnumerable <string> strs)
{
var maxLength = strs.Select(s => s.Length).Max();
ulong strSz = (ulong)strs.Count();
var buf = strs.SelectMany(s => s.PadRight(maxLength).ToCharArray()).ToArray();
ulong[] dimsa = new ulong[] { strSz, 1 };
/* Create the data space for the dataset. */
ulong[] dims = new ulong[] { strSz, (ulong)maxLength };
var spaceId = H5S.create_simple(2, dims, null);
/* Create the dataset. */
name = ToHdf5Name(name);
//var aId = H5S.create_simple(2, dimsa, null);
var aTypeId = H5T.copy(H5T.C_S1);
H5T.set_size(aTypeId, new IntPtr(2));
byte[] wdata = new byte[2 * buf.Length];
for (int i = 0; i < buf.Length; ++i)
{
wdata[2 * i] = (byte)buf[i];
}
var datasetId = H5D.create(groupId, name, H5T.FORTRAN_S1, spaceId);
GCHandle hnd = GCHandle.Alloc(wdata, GCHandleType.Pinned);
var result = H5D.write(datasetId, aTypeId, H5S.ALL, H5S.ALL, H5P.DEFAULT,
hnd.AddrOfPinnedObject());
hnd.Free();
H5D.close(datasetId);
H5S.close(spaceId);
H5T.close(aTypeId);
return(result);
}
public static string ReadAsciiString(hid_t groupId, string name)
{
var datatype = H5T.FORTRAN_S1;
//name = ToHdf5Name(name);
var datasetId = H5D.open(groupId, 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);
}
private static double[] ReadDataVector(hid_t fileLoc, string name)
{
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] * 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);
double[] val = new double[dims[0]];
for (int i = 0; i < (int)dims[0]; i++)
{
val[i] = BitConverter.ToDouble(rdata, i * 8);
}
return(val);
}
public static Array ReadPrimitiveAttributes <T>(hid_t groupId, string name) //where T : struct
{
Type type = typeof(T);
var datatype = GetDatatype(type);
var attributeId = H5A.open(groupId, name);
var spaceId = H5A.get_space(attributeId);
int rank = H5S.get_simple_extent_ndims(spaceId);
ulong[] maxDims = new ulong[rank];
ulong[] dims = new ulong[rank];
hid_t memId = H5S.get_simple_extent_dims(spaceId, dims, maxDims);
long[] lengths = dims.Select(d => Convert.ToInt64(d)).ToArray();
Array attributes = Array.CreateInstance(type, lengths);
var typeId = H5A.get_type(attributeId);
var mem_type = H5T.copy(datatype);
if (datatype == H5T.C_S1)
{
H5T.set_size(datatype, new IntPtr(2));
}
var propId = H5A.get_create_plist(attributeId);
memId = H5S.create_simple(rank, dims, maxDims);
GCHandle hnd = GCHandle.Alloc(attributes, GCHandleType.Pinned);
H5A.read(attributeId, datatype, hnd.AddrOfPinnedObject());
hnd.Free();
H5A.close(typeId);
H5A.close(attributeId);
H5S.close(spaceId);
return(attributes);
}
public void Create(string key, object value)
{
Host.With((id) =>
{
long dataspace = 0;
long typeId = 0;
long attributeId = 0;
try
{
if (value is Array)
{
var array = (Array)value;
dataspace = H5S.create_simple(array.Rank, array.Shape(), null);
throw new NotImplementedException("Scalar attributes only");
}
else
{
dataspace = H5S.create(H5S.class_t.SCALAR);
}
IntPtr nativeMemory;
if (value is String)
{
var str = (string)value;
typeId = H5T.copy(H5T.C_S1);
H5T.set_size(typeId, new IntPtr(str.Length));
nativeMemory = Marshal.StringToHGlobalAnsi(str);
}
else if (value is long)
{
var l = new long[] { (long)value };
typeId = H5T.copy(H5T.NATIVE_INT64);
nativeMemory = Marshal.AllocHGlobal(sizeof(long));
Marshal.Copy(l, 0, nativeMemory, 1);
}
else
{
throw new NotImplementedException("Unsupported attribute type: " + value.GetType().Name);
}
attributeId = H5A.create(id, key, typeId, dataspace);
H5A.write(attributeId, typeId, nativeMemory);
Marshal.FreeHGlobal(nativeMemory);
}
finally
{
if (attributeId > 0)
{
H5A.close(attributeId);
}
if (typeId > 0)
{
H5T.close(typeId);
}
if (dataspace > 0)
{
H5S.close(dataspace);
}
}
});
}
public static long GetHdfTypeIdFromType(long fileId, Type type)
{
Type elementType;
elementType = type.IsArray ? type.GetElementType() : type;
if (elementType == typeof(bool))
{
return(H5T.NATIVE_UINT8);
}
else if (elementType == typeof(Byte))
{
return(H5T.NATIVE_UINT8);
}
else if (elementType == typeof(SByte))
{
return(H5T.NATIVE_INT8);
}
else if (elementType == typeof(UInt16))
{
return(H5T.NATIVE_UINT16);
}
else if (elementType == typeof(Int16))
{
return(H5T.NATIVE_INT16);
}
else if (elementType == typeof(UInt32))
{
return(H5T.NATIVE_UINT32);
}
else if (elementType == typeof(Int32))
{
return(H5T.NATIVE_INT32);
}
else if (elementType == typeof(UInt64))
{
return(H5T.NATIVE_UINT64);
}
else if (elementType == typeof(Int64))
{
return(H5T.NATIVE_INT64);
}
else if (elementType == typeof(Single))
{
return(H5T.NATIVE_FLOAT);
}
else if (elementType == typeof(Double))
{
return(H5T.NATIVE_DOUBLE);
}
else if (elementType == typeof(string) || elementType == typeof(IntPtr))
{
long typeId = 0;
if (H5I.is_valid(fileId) > 0 && H5L.exists(fileId, "string_t") > 0)
{
typeId = H5T.open(fileId, "string_t");
}
else
{
typeId = H5T.copy(H5T.C_S1);
H5T.set_size(typeId, H5T.VARIABLE);
H5T.set_cset(typeId, H5T.cset_t.UTF8);
if (fileId > -1 && H5T.commit(fileId, "string_t", typeId) < 0)
{
throw new Exception(ErrorMessage.TypeConversionHelper_CouldNotCommitDataType);
}
}
return(typeId);
}
else if (elementType.IsValueType && !elementType.IsPrimitive && !elementType.IsEnum)
{
long typeId = 0;
if (H5I.is_valid(fileId) > 0 && H5L.exists(fileId, elementType.Name) > 0)
{
typeId = H5T.open(fileId, elementType.Name);
}
else
{
typeId = H5T.create(H5T.class_t.COMPOUND, new IntPtr(Marshal.SizeOf(elementType)));
foreach (FieldInfo fieldInfo in elementType.GetFields())
{
long fieldType = -1;
fieldType = TypeConversionHelper.GetHdfTypeIdFromType(fileId, fieldInfo.FieldType);
H5T.insert(typeId, fieldInfo.Name, Marshal.OffsetOf(elementType, fieldInfo.Name), fieldType);
if (H5I.is_valid(fieldType) > 0)
{
H5T.close(fieldType);
}
}
if (fileId > -1 && H5T.commit(fileId, elementType.Name, typeId) < 0)
{
throw new Exception(ErrorMessage.TypeConversionHelper_CouldNotCommitDataType);
}
}
return(typeId);
}
else
{
throw new NotSupportedException();
}
}
/// <summary>
/// Currently does not support arrays
/// </summary>
/// <typeparam name="T"></typeparam>
/// <param name="_objectId"></param>
/// <param name="_title"></param>
/// <param name="_value"></param>
/// <returns></returns>
public static Hdf5Attribute CreateAttribute <T>(Hdf5Identifier _objectId, string _title, T _value)
{
ulong[] sizes = new ulong[1] {
1
};
Hdf5Identifier dataspaceId;
Hdf5Identifier attributeId;
Hdf5Identifier typeId;
Hdf5Attribute attribute = null;
Type type = _value.GetType();
var datatype = TypeHelper.GetDataTypesEnum(type);
if (datatype != Hdf5DataTypes.String)
{
var tempType = TypeHelper.GetNativeType(datatype);
typeId = H5T.copy(tempType.Value).ToId();
var dataTypeObject = TypeHelper.GetDataTypeByType(typeId);
var status = H5T.set_order(typeId.Value, H5T.order_t.LE);
dataspaceId = H5S.create_simple(1, sizes, null).ToId();
attributeId = H5A.create(_objectId.Value, _title, typeId.Value, dataspaceId.Value).ToId();
if (attributeId.Value > 0)
{
WriteValue(dataTypeObject, attributeId, _value);
}
}
else
{
string tempValue = Convert.ToString(_value);
dataspaceId = H5S.create(H5S.class_t.SCALAR).ToId();
typeId = H5T.copy(H5T.C_S1).ToId();
int length = tempValue.Length + 1;
var result = H5T.set_size(typeId.Value, new IntPtr(length));
attributeId = H5A.create(_objectId.Value, _title, typeId.Value, dataspaceId.Value).ToId();
IntPtr valueArray = Marshal.StringToHGlobalAnsi(tempValue);
result = H5A.write(attributeId.Value, typeId.Value, valueArray);
Marshal.FreeHGlobal(valueArray);
}
H5S.close(dataspaceId.Value);
H5T.close(typeId.Value);
H5A.close(attributeId.Value);
if (attributeId.Value > 0)
{
attribute = new Hdf5Attribute
{
Value = _value,
Name = _title,
Id = attributeId
};
}
return(attribute);
}
public static bool WriteVariableStringAttribute(hid_t hid, string key, IEnumerable <string> values, bool utf8)
{
if (key == null)
{
throw new ArgumentNullException("key");
}
if (values == null)
{
throw new ArgumentNullException("values");
}
var exists = H5A.exists(hid, key);
if (exists < 0)
{
throw new Exception("H5A.exists failed");
}
if (exists == 0) // Attribute doesn't exist
{
#if true
var type = H5T.create(H5T.class_t.STRING, H5T.VARIABLE);
if (type < 0)
{
throw new Exception("Failed to create string type");
}
#else
var type = H5T.copy(H5T.C_S1);
if (type < 0)
{
throw new Exception("Failed to create string type");
}
if (H5T.set_size(type, H5T.VARIABLE) < 0)
{
H5T.close(type);
throw new Exception("Failed to set type size");
}
#endif
if (utf8)
{
if (H5T.set_cset(type, H5T.cset_t.UTF8) < 0)
{
H5T.close(type);
throw new Exception("Failed to set cset");
}
}
if (H5T.set_strpad(type, H5T.str_t.NULLTERM) < 0)
{
H5T.close(type);
throw new Exception("Failed to set strpad");
}
var space = values.Count() == 1 ? H5S.create(H5S.class_t.SCALAR)
: H5S.create_simple(1, new ulong[1] {
(ulong)values.Count()
}, null);
if (space < 0)
{
H5T.close(type);
throw new Exception("Failed to create data space");
}
var attribute = H5A.create(hid, key, type, space);
H5S.close(space);
if (attribute < 0)
{
H5T.close(type);
throw new Exception(string.Format("Failed to create attribute \"{0}\"", key));
}
var pinnedObjects = new PinnedObject[values.Count()];
var data = new IntPtr[values.Count()];
int count = 0;
foreach (string str in values)
{
var bytes = str.ToBytes(utf8);
pinnedObjects[count] = new PinnedObject(bytes);
data[count] = pinnedObjects[count];
count += 1;
}
H5A.write(attribute, type, new PinnedObject(data));
H5T.close(type);
H5A.close(attribute);
}
else
{
// Attribute exists.
var attribute = H5A.open(hid, key);
if (attribute < 0)
{
throw new Exception(string.Format("Failed to open attribute \"{0}\"", key));
}
var type = H5A.get_type(attribute);
if (type < 0)
{
H5A.close(attribute);
throw new Exception("Failed to get data type");
}
var pinnedObjects = new PinnedObject[values.Count()];
var data = new IntPtr[values.Count()];
int count = 0;
foreach (string str in values)
{
var bytes = str.ToBytes(utf8);
pinnedObjects[count] = new PinnedObject(bytes);
data[count] = pinnedObjects[count];
count += 1;
}
H5A.write(attribute, type, new PinnedObject(data));
H5T.close(type);
H5A.close(attribute);
}
return(true);
}
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 + null terminate (ASCII)
var typeIdFixed_nullterm = H5T.copy(H5T.C_S1);
res = H5T.set_size(typeIdFixed_nullterm, new IntPtr(4));
res = H5T.set_cset(typeIdFixed_nullterm, H5T.cset_t.ASCII);
res = H5T.set_strpad(typeIdFixed_nullterm, H5T.str_t.NULLTERM);
var dataFixed_nullterm = new string[] { "00\00", "11\0 ", "22\0 ", "3\0 ", "44 \0", "555\0", "66 \0", "77\0 ", " \0 ", "AA \0", "ZZ \0", "!!\0 " };
var dataFixedChar_nullterm = dataFixed_nullterm
.SelectMany(value => Encoding.ASCII.GetBytes(value))
.ToArray();
TestUtils.Add(container, fileId, "string", "fixed+nullterm", typeIdFixed_nullterm, dataFixedChar_nullterm.AsSpan(), dims);
res = H5T.close(typeIdFixed_nullterm);
// fixed length string attribute + null padding (ASCII)
var typeIdFixed_nullpad = H5T.copy(H5T.C_S1);
res = H5T.set_size(typeIdFixed_nullpad, new IntPtr(4));
res = H5T.set_cset(typeIdFixed_nullpad, H5T.cset_t.ASCII);
res = H5T.set_strpad(typeIdFixed_nullpad, H5T.str_t.NULLPAD);
var dataFixed_nullpad = new string[] { "0\00\0", "11\0\0", "22\0\0", "3 \0\0", " 4\0\0", "55 5", "66\0\0", "77\0\0", " \0\0", "AA\0\0", "ZZ\0\0", "!!\0\0" };
var dataFixedChar_nullpad = dataFixed_nullpad
.SelectMany(value => Encoding.ASCII.GetBytes(value))
.ToArray();
TestUtils.Add(container, fileId, "string", "fixed+nullpad", typeIdFixed_nullpad, dataFixedChar_nullpad.AsSpan(), dims);
res = H5T.close(typeIdFixed_nullpad);
// fixed length string attribute + space padding (ASCII)
var typeIdFixed_spacepad = H5T.copy(H5T.C_S1);
res = H5T.set_size(typeIdFixed_spacepad, new IntPtr(4));
res = H5T.set_cset(typeIdFixed_spacepad, H5T.cset_t.ASCII);
res = H5T.set_strpad(typeIdFixed_spacepad, H5T.str_t.SPACEPAD);
var dataFixed_spacepad = new string[] { "00 ", "11 ", "22 ", "3 ", " 4 ", "55 5", "66 ", "77 ", " ", "AA ", "ZZ ", "!! " };
var dataFixedChar_spacepad = dataFixed_spacepad
.SelectMany(value => Encoding.ASCII.GetBytes(value))
.ToArray();
TestUtils.Add(container, fileId, "string", "fixed+spacepad", typeIdFixed_spacepad, dataFixedChar_spacepad.AsSpan(), dims);
res = H5T.close(typeIdFixed_spacepad);
// 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);
res = H5T.set_strpad(typeIdVar, H5T.str_t.NULLPAD);
var dataVar = new string[] { "001", "11", "22", "33", "44", "55", "66", "77", " ", "AA", "ZZ", "!!" };
var dataVarChar = dataVar
.SelectMany(value => Encoding.ASCII.GetBytes(value + '\0'))
.ToArray();
fixed(byte *dataVarPtr = dataVarChar)
{
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, "string", "variable", typeIdVar, dataVarAddressesPtr, dims);
}
}
res = H5T.close(typeIdVar);
// variable length string attribute + space padding (ASCII)
var typeIdVar_spacepad = H5T.copy(H5T.C_S1);
res = H5T.set_size(typeIdVar_spacepad, H5T.VARIABLE);
res = H5T.set_cset(typeIdVar_spacepad, H5T.cset_t.ASCII);
res = H5T.set_strpad(typeIdVar_spacepad, H5T.str_t.SPACEPAD);
var dataVar_spacepad = new string[] { "001 ", "1 1 ", "22 ", "33", "44", "55", "66", "77", " ", "AA", "ZZ", "!!" };
var dataVarChar_spacepad = dataVar_spacepad
.SelectMany(value => Encoding.ASCII.GetBytes(value + '\0'))
.ToArray();
fixed(byte *dataVarPtr_spacepad = dataVarChar_spacepad)
{
var basePtr = new IntPtr(dataVarPtr_spacepad);
var addresses = new IntPtr[]
{
IntPtr.Add(basePtr, 0), IntPtr.Add(basePtr, 6), IntPtr.Add(basePtr, 11), 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), IntPtr.Add(basePtr, 37), IntPtr.Add(basePtr, 40)
};
fixed(void *addressesPtr = addresses)
{
TestUtils.Add(container, fileId, "string", "variable+spacepad", typeIdVar_spacepad, addressesPtr, dims);
}
}
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);
res = H5T.set_strpad(typeIdVarUTF8, H5T.str_t.NULLPAD);
var dataVarUTF8 = new string[] { "00", "111", "22", "33", "44", "55", "66", "77", " ", "ÄÄ", "的的", "!!" };
var dataVarCharUTF8 = dataVarUTF8
.SelectMany(value => Encoding.UTF8.GetBytes(value + '\0'))
.ToArray();
fixed(byte *dataVarPtrUTF8 = dataVarCharUTF8)
{
var basePtr = new IntPtr(dataVarPtrUTF8);
var addresses = new IntPtr[]
{
IntPtr.Add(basePtr, 0), IntPtr.Add(basePtr, 3), 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, 33), IntPtr.Add(basePtr, 40)
};
fixed(void *addressesPtr = addresses)
{
TestUtils.Add(container, fileId, "string", "variableUTF8", typeIdVarUTF8, addressesPtr, dims);
}
}
}
private static long GetHdfTypeIdFromType(Type type)
{
var elementType = type.IsArray ? type.GetElementType() : type;
if (elementType == typeof(bool))
{
return(H5T.NATIVE_UINT8);
}
else if (elementType == typeof(byte))
{
return(H5T.NATIVE_UINT8);
}
else if (elementType == typeof(sbyte))
{
return(H5T.NATIVE_INT8);
}
else if (elementType == typeof(ushort))
{
return(H5T.NATIVE_UINT16);
}
else if (elementType == typeof(short))
{
return(H5T.NATIVE_INT16);
}
else if (elementType == typeof(uint))
{
return(H5T.NATIVE_UINT32);
}
else if (elementType == typeof(int))
{
return(H5T.NATIVE_INT32);
}
else if (elementType == typeof(ulong))
{
return(H5T.NATIVE_UINT64);
}
else if (elementType == typeof(long))
{
return(H5T.NATIVE_INT64);
}
else if (elementType == typeof(float))
{
return(H5T.NATIVE_FLOAT);
}
else if (elementType == typeof(double))
{
return(H5T.NATIVE_DOUBLE);
}
// issues: https://en.wikipedia.org/wiki/Long_double
//else if (elementType == typeof(decimal))
// return H5T.NATIVE_LDOUBLE;
else if (elementType.IsEnum)
{
var baseTypeId = TestUtils.GetHdfTypeIdFromType(Enum.GetUnderlyingType(elementType));
var typeId = H5T.enum_create(baseTypeId);
foreach (var value in Enum.GetValues(type))
{
var value_converted = Convert.ToInt64(value);
var name = Enum.GetName(type, value_converted);
var handle = GCHandle.Alloc(value_converted, GCHandleType.Pinned);
H5T.enum_insert(typeId, name, handle.AddrOfPinnedObject());
}
return(typeId);
}
else if (elementType == typeof(string) || elementType == typeof(IntPtr))
{
var typeId = H5T.copy(H5T.C_S1);
H5T.set_size(typeId, H5T.VARIABLE);
H5T.set_cset(typeId, H5T.cset_t.UTF8);
return(typeId);
}
else if (elementType.IsValueType && !elementType.IsPrimitive)
{
var typeId = H5T.create(H5T.class_t.COMPOUND, new IntPtr(Marshal.SizeOf(elementType)));
foreach (var fieldInfo in elementType.GetFields())
{
var fieldType = TestUtils.GetHdfTypeIdFromType(fieldInfo.FieldType);
var attribute = fieldInfo.GetCustomAttribute <H5NameAttribute>(true);
var hdfFieldName = attribute is not null ? attribute.Name : fieldInfo.Name;
H5T.insert(typeId, hdfFieldName, Marshal.OffsetOf(elementType, fieldInfo.Name), fieldType);
if (H5I.is_valid(fieldType) > 0)
{
H5T.close(fieldType);
}
}
return(typeId);
}
else
{
throw new NotSupportedException();
}
}
public static void ClassInit(TestContext testContext)
{
// create test files which persists across file tests
m_v0_class_file = Utilities.H5TempFile(ref m_v0_class_file_name,
H5F.libver_t.EARLIEST);
Assert.IsTrue(m_v0_class_file >= 0);
m_v2_class_file = Utilities.H5TempFile(ref m_v2_class_file_name);
Assert.IsTrue(m_v2_class_file >= 0);
m_space_null = H5S.create(H5S.class_t.NULL);
Assert.IsTrue(m_space_null >= 0);
m_space_scalar = H5S.create(H5S.class_t.SCALAR);
Assert.IsTrue(m_space_scalar >= 0);
// create two datasets of the extended ASCII character set
// store as H5T.FORTRAN_S1 -> space padding
hsize_t[] dims = { 256 };
hid_t space = H5S.create_simple(1, dims, null);
m_v0_ascii_dset = H5D.create(m_v0_class_file, "ASCII",
H5T.FORTRAN_S1, space);
m_v2_ascii_dset = H5D.create(m_v2_class_file, "ASCII",
H5T.FORTRAN_S1, space);
Assert.IsTrue(H5S.close(space) >= 0);
// we write from C and must provide null-terminated strings
byte[] wdata = new byte[512];
for (int i = 0; i < 256; ++i)
{
wdata[2 * i] = (byte)i;
}
hid_t mem_type = H5T.copy(H5T.C_S1);
Assert.IsTrue(H5T.set_size(mem_type, new IntPtr(2)) >= 0);
GCHandle hnd = GCHandle.Alloc(wdata, GCHandleType.Pinned);
Assert.IsTrue(H5D.write(m_v0_ascii_dset, mem_type, H5S.ALL,
H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject()) >= 0);
Assert.IsTrue(H5D.write(m_v2_ascii_dset, mem_type, H5S.ALL,
H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject()) >= 0);
hnd.Free();
Assert.IsTrue(H5T.close(mem_type) >= 0);
// create UTF-8 encoded test datasets
hid_t dtype = H5T.create(H5T.class_t.STRING, H5T.VARIABLE);
Assert.IsTrue(H5T.set_cset(dtype, H5T.cset_t.UTF8) >= 0);
Assert.IsTrue(H5T.set_strpad(dtype, H5T.str_t.SPACEPAD) >= 0);
hid_t dspace = H5S.create_simple(1,
new hsize_t[] { (hsize_t)m_utf8strings.Count }, null);
m_v0_utf8_dset = H5D.create(m_v0_class_file, "UTF-8", dtype, dspace);
Assert.IsTrue(m_v0_utf8_dset >= 0);
m_v2_utf8_dset = H5D.create(m_v2_class_file, "UTF-8", dtype, dspace);
Assert.IsTrue(m_v2_utf8_dset >= 0);
GCHandle[] hnds = new GCHandle[m_utf8strings.Count];
IntPtr[] wdata1 = new IntPtr[m_utf8strings.Count];
for (int i = 0; i < m_utf8strings.Count; ++i)
{
hnds[i] = GCHandle.Alloc(
Encoding.UTF8.GetBytes((string)m_utf8strings[i]),
GCHandleType.Pinned);
wdata1[i] = hnds[i].AddrOfPinnedObject();
}
hnd = GCHandle.Alloc(wdata1, GCHandleType.Pinned);
Assert.IsTrue(H5D.write(m_v0_utf8_dset, dtype, H5S.ALL, H5S.ALL,
H5P.DEFAULT, hnd.AddrOfPinnedObject()) >= 0);
Assert.IsTrue(H5D.write(m_v2_utf8_dset, dtype, H5S.ALL, H5S.ALL,
H5P.DEFAULT, hnd.AddrOfPinnedObject()) >= 0);
hnd.Free();
for (int i = 0; i < m_utf8strings.Count; ++i)
{
hnds[i].Free();
}
Assert.IsTrue(H5S.close(dspace) >= 0);
Assert.IsTrue(H5T.close(dtype) >= 0);
}