Hi Johan,
Everything in your code seems to be fine, but since your initial dataset
X-dimension is "0" (no rows when creating dataset) you have to call:
H5D.set_extent(datasetId, count);
right after you defined a new space dimensions in "count".
See also my minimal working example in C++ (but using C API):
int rank = 2;
int nCols = 30;
int nRows = 5;
hsize_t tdims[rank] = {0, nCols};
hsize_t maxdims[rank] = {H5S_UNLIMITED, nCols};
hid_t space_2d = H5Screate_simple (rank, tdims, maxdims);
hid_t plist = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_layout(plist, H5D_CHUNKED);
hsize_t chunk[rank] = {1, nCols};
H5Pset_chunk(plist, rank, chunk);
hid_t datasetId = H5Dcreate(file_id, "TestDataset",
H5T_NATIVE_DOUBLE, space_2d, H5P_DEFAULT, plist, H5P_DEFAULT);
hsize_t newdims[rank] = {nRows, nCols};
H5Dset_extent(datasetId, newdims);
hid_t newspace = H5Dget_space(datasetId);
hsize_t offset[rank] = {0, 0};
H5Sselect_hyperslab(newspace, H5S_SELECT_SET, offset, NULL,
newdims, NULL);
hid_t tmemspace = H5Screate_simple(rank, newdims, NULL);
double data[nCols * nRows];
double step = 1.1;
for(int r = 0; r < nRows; r++)
{
for(int c = 0; c < nCols; c++)
{
data[c + r * nCols] = step;
step += 1.1;
}
}
uint8_t *data_bytes = reinterpret_cast<uint8_t*>(data);
H5Dwrite (datasetId, H5T_NATIVE_DOUBLE, tmemspace, newspace,
H5P_DEFAULT, data_bytes);
H5Sclose(newspace);
H5Sclose(tmemspace);
H5Dclose(datasetId);
H5Pclose(plist);
H5Sclose(space_2d);
Best regards,
Rafal
W dniu 2017-10-19 o 09:33, Johan Lindberg pisze:
Hi Rafael,
Thank you for your reply!
I am using Visual Studio (C#) and HDF5 P/Invoke. While the syntax is a
bit different from C/C++, the HDF5 functions should do the same.
I am indeed setting the type argument to the native double type. I paste
my (simplified yet still quite lengthy) code below.
It is the status in the try block in the very end that returns -1. This
works fine if I pass the double[] valuesOneDim to H5D.write instead of
the byte[] byteData.
// Create a H5F file and H5G group (not included)
hid_t groupId = ...
// Create dataspace and dataset:
int nCols = 30;
int nRows = 5;
htri_t rank = 2;
ulong[] dims = new ulong[2] { 0, nCols };
ulong?[] maxDims = new ulong[2] { H5S.UNLIMITED, nCols };
string name = "TestDataset";
hid_t dataspaceId = H5S.create_simple(rank, dims, maxDims);
hid_t pList = H5P.create(H5P.DATASET_CREATE);
H5P.set_layout(pList, H5D.layout_t.CHUNKED);
H5P.set_chunk(pList, rank, new ulong[] { 1, (ulong)maxDims[1] });
hid_t datasetId = H5D.create(groupId, name, H5T.NATIVE_DOUBLE, dataspaceId,
H5P.DEFAULT, pList, H5P.DEFAULT);
H5P.close(pList);
// Generate a 2D (5x30) random double array and converting it to a 1D
byte array.
Random random = new Random();
double[,] values = new double[nCols, nRows];
double[] valuesOneDim = new double[nCols * nRows];
int nBytes = 8;
byte[] byteData = new byte[nCols * nRows * nBytes];
for (int i = 0; i < nCols; i++)
{
for (int j = 0; j < nRows; j++)
{
values[i, j] = random.NextDouble();
valuesOneDim[i + nCols * j] = values[i, j];
byte[] thisByteValue = BitConverter.GetBytes(values[i, j]);
for (int k = 0; k < nBytes; k++)
{
byteData[k + nBytes * (i + nCols * j)] = thisByteValue[k];
}
}
}
// Write byte array to dataset
htri_t status = -1;
int arrayCols = (htri_t)(dims[1]);
int existingRows = (htri_t)(dims[0]);
int appendRows = data.GetLength(0) / Marshal.SizeOf(typeof(T)) /
arrayCols; // This number is 5, just like nRows.
htri_t nBytes = Marshal.SizeOf(typeof(T)) * arrayCols * appendRows; // =
5*30*8=1200
ulong[] appendDims = new ulong[] { (ulong)appendRows, (ulong)arrayCols
}; // [5, 30]
hid_t memSpaceId = H5S.create_simple(2, appendDims, null);
ulong[] start = new ulong[2] { (ulong)existingRows, 0 }; // [0, 0]
ulong[] count = new ulong[2] { (ulong)appendRows, (ulong)arrayCols }; //
[5, 30]
dataspaceId = H5D.get_space(datasetId);
H5S.select_hyperslab(dataspaceId, H5S.seloper_t.SET, start, null, count,
null);
GCHandle handle = default(GCHandle);
try
{
handle = GCHandle.Alloc(byteData, GCHandleType.Pinned);
using (SafeArrayBuffer buffer = new
SafeArrayBuffer(Marshal.AllocHGlobal(nBytes)))
{
Marshal.Copy(byteData, 0, buffer.DangerousGetHandle(), nBytes);
status = H5D.write(datasetId, H5T.NATIVE_DOUBLE, memSpaceId,
dataspaceId, H5P.DEFAULT, buffer.DangerousGetHandle());
}
}
finally
{
handle.Free();
}
// Close dataspaces, datasets, types, etc (not included).
...
Hi Johan,
The second argument to H5Dwrite function (referring to C API, not C++)
sets the type of single element which is expected in data buffer. If you
set this to H5T_NATIVE_DOUBLE everything should be fine and data should
be properly written since data buffer is just a pointer (void*).
https://support.hdfgroup.org/HDF5/doc/RM/RM_H5D.html#Dataset-Write
<https://support.hdfgroup.org/HDF5/doc/RM/RM_H5D.html#Dataset-Write>
Usually -1 status means that you messed something with memory space and
file space (3rd and 4th argument of H5Dwrite) and/or dataset dimensions.
Please send some of your code examples (including how dataset is
created) for further investigation...
Regards,
Rafal
W dniu 2017-10-18 o?14:21, Johan Lindberg pisze:
> Hi,
>
> Is there a way to write raw binary byte array data to an existing
> dataset of a different type? E.g., if I have a byte array that
> represents an array of doubles (the byte array thus has 8 times
as many
> elements as the double array, where each set of 8 bytes represents a
> double), can I somehow write that data to a double dataset in an HDF5
> file? Trying this the na?ve way with HDF.write just returns a -1
status.
>
> The reason why I don't just convert it to a double array before
writing
> is that I have an instrument which returns all its data in byte
arrays,
> no matter the type, and then I'd have to write a converter for
each of
> the 10 different types it output in.
>
> Thank you,
> Johan Lindberg
>
> --
> Dr. Johan E. Lindberg
>
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@lists.hdfgroup.org <mailto:Hdf-forum@lists.hdfgroup.org>
>
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
<http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org>
> Twitter: https://twitter.com/hdf5
>
------------------------------
Subject: Digest Footer
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org <mailto:Hdf-forum@lists.hdfgroup.org>
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
<http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org>
------------------------------
End of Hdf-forum Digest, Vol 100, Issue 13
******************************************
--
Dr. Johan E. Lindberg
Mobile phone: +46 (0)76-209 14 13
e-mail: jolin...@gmail.com <mailto:jolin...@gmail.com>
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
