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[Issue #333] Change single value writing to use SCALAR spaces #337

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[Issue #333] Change single value writing to use SCALAR spaces #337

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34cfd87
[Issue #17] Change single value writing to use SCALAR spaces instead …
Nov 17, 2023
91032d8
Correct the implementation of WriteAsciiString and WriteOneValue so t…
Nov 21, 2023
05a31c2
Rework how Ascii strings are read out based on the implementation of …
Nov 21, 2023
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71 changes: 50 additions & 21 deletions HDF5-CSharp/Hdf5Dataset.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -271,27 +271,56 @@ public static (bool success, Array result) ReadDataset<T>(long groupId, string n
return dsetRW.ReadArray<T>(groupId, name, alternativeName, mandatory);
}

/// <summary>
/// Writes one value to a hdf5 file
/// </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>
/// <param name="dset">The dataset</param>
/// <returns>status of the write method</returns>
public static (int success, long CreatedgroupId) WriteOneValue<T>(long groupId, string name, T dset, Dictionary<string, List<string>> attributes)
{
if (typeof(T) == typeof(string))
//WriteStrings(groupId, name, new string[] { dset.ToString() });
{
return dsetRW.WriteArray(groupId, name, new T[1] { dset }, attributes);
}

Array oneVal = new T[1, 1] { { dset } };
return dsetRW.WriteArray(groupId, name, oneVal, attributes);
}

public static void WriteDataset(long groupId, string name, Array collection)
/// <summary>
/// Writes one value to a hdf5 file
/// </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>
/// <param name="dset">The dataset</param>
/// <returns>status of the write method</returns>
public static (int success, long CreatedgroupId) WriteOneValue<T>(long groupId, string name, T value, Dictionary<string, List<string>> attributes)
{
var spaceId = H5S.create(H5S.class_t.SCALAR);
var datatype = GetDatatype(typeof(T));
var typeId = H5T.copy(datatype);

GCHandle hnd;
if (datatype == H5T.C_S1 || datatype == H5T.FORTRAN_S1)
{
int stringLen = (value as string).Length;

H5T.set_size(typeId, new IntPtr(stringLen));

byte[] strByteArray = new byte[stringLen + 1];
// Write the string to the buffer, with the last element being 0 as the string terminator
for (int i = 0; i < stringLen; ++i)
{
strByteArray[i] = Convert.ToByte((value as string)[i]);
}
hnd = GCHandle.Alloc(strByteArray, GCHandleType.Pinned);
}
else
{
hnd = GCHandle.Alloc(value, GCHandleType.Pinned);
}

string normalizedName = Hdf5Utils.NormalizedName(name);
var datasetId = Hdf5Utils.GetDatasetId(groupId, normalizedName, typeId, spaceId, H5P.DEFAULT);
if (datasetId == -1L)
{
return (-1, -1L);
}

var result = H5D.write(datasetId, typeId, H5S.ALL, H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
H5D.close(datasetId);
H5S.close(spaceId);
H5T.close(typeId);
return (result, datasetId);
}

public static void WriteDataset(long groupId, string name, Array collection)
{
dsetRW.WriteArray(groupId, name, collection, new Dictionary<string, List<string>>());
}
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75 changes: 29 additions & 46 deletions HDF5-CSharp/Hdf5Strings.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -110,68 +110,51 @@ public static (int success, long CreatedgroupId) WriteStrings(long groupId, stri

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);
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;

int strLength = str.Length;
ulong[] dims = { (ulong)strLength, 1 };
var memId = H5T.copy(H5T.C_S1);
// Set the size needed for the string. Leave one extra space for a null-terminated string
H5T.set_size(memId, new IntPtr(strLength + 1));

/* Create the dataset. */
//name = ToHdf5Name(name);
var datasetId = H5D.create(groupId, Hdf5Utils.NormalizedName(name), memId, spaceScalarId);

var spaceId = H5S.create_simple(1, dims, null);
var datasetId = H5D.create(groupId, Hdf5Utils.NormalizedName(name), H5T.FORTRAN_S1, spaceId);
H5S.close(spaceId);
byte[] wdata = new byte[strLength];
// Write the string to the buffer, with the last element being 0 as the string terminator
for (int i = 0; i < strLength; ++i)
{
wdata[i] = Convert.ToByte(str[i]);
}

// we write from C and must provide null-terminated strings
GCHandle hnd = GCHandle.Alloc(wdata, GCHandleType.Pinned);

byte[] wdata = new byte[strLength * 2];

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));
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;
}
int result = H5D.write(datasetId, memId, H5S.ALL, H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
H5S.close(spaceScalarId);
H5T.close(memId);
H5D.close(datasetId);
return result;
}

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];

ulong spaceNeeded = H5D.get_storage_size(datasetId);
byte[] wdata = new byte[spaceNeeded];

var memId = H5T.copy(H5T.C_S1);
H5T.set_size(memId, new IntPtr(2));
GCHandle hnd = GCHandle.Alloc(wdata, GCHandleType.Pinned);
int resultId = H5D.read(datasetId, memId, H5S.ALL,
var memId = H5T.copy(H5T.C_S1);
H5T.set_size(memId, new IntPtr((int)spaceNeeded));

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();
// Remove the null termination of the string
wdata = wdata.Where(b => b != 0).ToArray();
string result = Encoding.ASCII.GetString(wdata);

H5T.close(memId);
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