public void H5Sget_select_hyper_blocklistTest1()
{
hsize_t[] dims = { 1, 2, 3 };
hid_t space = H5S.create_simple(dims.Length, dims, dims);
Assert.IsTrue(space > 0);
hsize_t[] start = { 0, 0, 0 };
hsize_t[] count = { 1, 1, 1 };
hsize_t[] block = { 1, 2, 3 };
Assert.IsTrue(
H5S.select_hyperslab(space, H5S.seloper_t.SET, start, null,
count, block) >= 0);
Assert.IsTrue(H5S.get_select_hyper_nblocks(space) == 1);
hsize_t[] buf = new hsize_t [2 * dims.Length];
Assert.IsTrue(
H5S.get_select_hyper_blocklist(space, 0, 1, buf) >= 0);
for (int i = 0; i < dims.Length; ++i)
{
buf[i] = 0;
buf[i + 3] = dims[i] - 1;
}
Assert.IsTrue(H5S.close(space) >= 0);
}
public void Put(Array data, ulong[] location = null)
{
ulong[] shape = data.Shape();
WithDataSpace((h5Ref, dsRef) =>
{
long memDataSpace = H5S.ALL;
if (location != null)
{
int selection = H5S.select_none(dsRef);
if (selection < 0)
{
throw new H5SSException("Couldn't clear dataspace selection");
}
ulong[] stride = Ones(shape.Length);
selection = H5S.select_hyperslab(dsRef,
H5S.seloper_t.SET,
location,
stride,
stride,
shape
);
if (selection < 0)
{
throw new H5SSException("Couldn't select hyperslab");
}
memDataSpace = H5S.create_simple(shape.Length, shape, shape);
}
IntPtr iPtr;
var effectiveSize = data.Length * ElementSize;
//if (DataType == HDF5DataType.String)
//{
// // Convert to byte array...
//}
//else
//{
//}
var dtype = H5D.get_type(h5Ref); // Return?
iPtr = CreateNativeArray(data, dtype);
// copy to unmanaged array?
var success = H5D.write(h5Ref, dtype, memDataSpace, dsRef, H5P.DEFAULT, iPtr);
H5T.close(dtype);
if (location != null)
{
H5S.close(memDataSpace);
}
Marshal.FreeHGlobal(iPtr);
if (success < 0)
{
throw new H5SSException(string.Format("Couldn't write to dataset: {0}", this.Path));
}
});
}
public void SelectHyperslab(ulong[] start, ulong[] stride, ulong[] count, ulong[] block)
{
if (H5S.select_hyperslab(ID, H5S.seloper_t.SET, start, stride, count, block) < 0)
{
throw new H5LibraryException($"H5S.select_hyperslab() returned an ERROR");
}
}
private static void AppendData <T>(hid_t dataSet, T[] data, ref int rows)
{
var fileSpace = H5D.get_space(dataSet);
if (fileSpace < 0)
{
throw new Exception("Failed to get data space of data set.");
}
var offset = new ulong[] { (ulong)rows };
var count = new ulong[] { (ulong)data.Length };
if (H5S.select_hyperslab(fileSpace, H5S.seloper_t.SET, offset, null, count, null) < 0)
{
throw new Exception("H5S.select_hyperslab failed.");
}
var memSpace = H5S.create_simple(1, count, null);
if (memSpace < 0)
{
throw new Exception("H5S.create_simple failed.");
}
if (H5D.write(dataSet, NumericTypeToHDF5Type <T>(), memSpace, fileSpace, H5P.DEFAULT, new PinnedObject(data)) < 0)
{
throw new Exception("H5D.write failed.");
}
H5S.close(memSpace);
H5S.close(fileSpace);
rows += data.Length;
}
private unsafe void WriteData(ulong fileOffset, ulong bufferOffset, ulong length, ChannelContext channelContext)
{
Contract.Requires(channelContext != null, nameof(channelContext));
long groupId = -1;
long datasetId = -1;
long dataspaceId = -1;
long dataspaceId_Buffer = -1;
try
{
groupId = H5G.open(_fileId, $"/{ channelContext.ChannelDescription.ChannelName }");
var datasetName = $"dataset_{ channelContext.ChannelDescription.DatasetName.Replace(" ", "_") }";
datasetId = H5D.open(groupId, datasetName);
dataspaceId = H5D.get_space(datasetId);
dataspaceId_Buffer = H5S.create_simple(1, new ulong[] { length }, null);
var simpleBuffers = channelContext.Buffer.ToSimpleBuffer();
// dataset
H5S.select_hyperslab(dataspaceId,
H5S.seloper_t.SET,
new ulong[] { fileOffset },
new ulong[] { 1 },
new ulong[] { 1 },
new ulong[] { length });
var offset = (int)bufferOffset * simpleBuffers.ElementSize;
var buffer = simpleBuffers.RawBuffer[offset..];
public void H5RcreateTest4()
{
byte[] path =
Encoding.UTF8.GetBytes(String.Join("/", m_utf8strings));
// make room for the trailling \0
byte[] name = new byte[path.Length + 1];
Array.Copy(path, name, path.Length);
hsize_t[] dims = new hsize_t[] { 10, 20 };
hid_t space = H5S.create_simple(2, dims, null);
Assert.IsTrue(space >= 0);
hid_t dset = H5D.create(m_v2_test_file, name, H5T.STD_I32LE, space,
m_lcpl_utf8);
Assert.IsTrue(dset >= 0);
hsize_t[] start = { 5, 10 };
hsize_t[] count = { 1, 1 };
hsize_t[] block = { 2, 4 };
Assert.IsTrue(
H5S.select_hyperslab(space, H5S.seloper_t.SET, start, null,
count, block) >= 0);
byte[] refer = new byte[H5R.DSET_REG_REF_BUF_SIZE];
GCHandle hnd = GCHandle.Alloc(refer, GCHandleType.Pinned);
Assert.IsTrue(
H5R.create(hnd.AddrOfPinnedObject(), m_v2_test_file, name,
H5R.type_t.DATASET_REGION, space) >= 0);
ssize_t size = H5R.get_name(m_v2_test_file,
H5R.type_t.DATASET_REGION, hnd.AddrOfPinnedObject(),
(byte[])null, IntPtr.Zero);
Assert.IsTrue(size.ToInt32() == name.Length);
byte[] buf = new byte[size.ToInt32() + 1];
size = H5R.get_name(m_v2_test_file, H5R.type_t.DATASET_REGION,
hnd.AddrOfPinnedObject(), buf, new IntPtr(buf.Length));
Assert.IsTrue(size.ToInt32() == name.Length);
// we need to account for the leading "/", which was not included
// in path
for (int i = 0; i < name.Length; ++i)
{
Assert.IsTrue(name[i] == buf[i + 1]);
}
hid_t sel = H5R.get_region(dset, H5R.type_t.DATASET_REGION,
hnd.AddrOfPinnedObject());
Assert.IsTrue(sel >= 0);
hnd.Free();
Assert.IsTrue(H5S.extent_equal(space, sel) > 0);
Assert.IsTrue(H5S.get_select_hyper_nblocks(space)
== H5S.get_select_hyper_nblocks(sel));
Assert.IsTrue(H5S.close(sel) >= 0);
Assert.IsTrue(H5D.close(dset) >= 0);
Assert.IsTrue(H5S.close(space) >= 0);
}
/// <summary>
/// WARNING: ADVANCED USE ONLY!! Loads a 2D generic dataset from an H5 file.
/// The generic loaders only loads data in non-Unity friendly types, such as bytes, uints, longs etc...
/// You'll have to know the correct cast to retrieve usable data.
///
/// Created With help from https://github.com/LiorBanai/HDF5-CSharp/blob/master/HDF5-CSharp/Hdf5Dataset.cs
/// </summary>
/// <param name="filePath"></param>
/// <param name="datasetName"></param>
/// <typeparam name="T"></typeparam>
/// <returns></returns>
/// <exception cref="FileNotFoundException"></exception>
static T[,] Load2DDataset <T>(string filePath, string datasetName)
{
if (!File.Exists(filePath))
{
throw new FileNotFoundException($"Loading dataset {datasetName} from file that doesn't exist {filePath}");
}
long fileId = H5F.open(filePath, H5F.ACC_RDONLY);
T[,] resultArray = new T[2, 2];
try {
ulong[] start = { 0, 0 };
ulong[] count = { 0, 0 };
long datasetId = H5D.open(fileId, datasetName);
var datatype = H5D.get_type(datasetId);
var spaceId = H5D.get_space(datasetId);
int rank = H5S.get_simple_extent_ndims(spaceId);
ulong[] maxDims = new ulong[rank];
ulong[] dims = new ulong[rank];
H5S.get_simple_extent_dims(spaceId, dims, maxDims);
count[0] = dims[0];
count[1] = dims[1];
// Define file hyperslab.
long status = H5S.select_hyperslab(spaceId, H5S.seloper_t.SET, start, null, count, null);
// Define the memory dataspace.
resultArray = new T[dims[0], dims[1]];
var memId = H5S.create_simple(rank, dims, null);
// Define memory hyperslab.
status = H5S.select_hyperslab(memId, H5S.seloper_t.SET, start, null,
count, null);
// Read data from hyperslab in the file into the hyperslab in
// memory and display.
GCHandle handle = GCHandle.Alloc(resultArray, GCHandleType.Pinned);
try {
H5D.read(datasetId, datatype, memId, spaceId,
H5P.DEFAULT, handle.AddrOfPinnedObject());
}
finally {
handle.Free();
H5S.close(status);
H5S.close(memId);
H5S.close(spaceId);
H5D.close(datatype);
H5D.close(datasetId);
}
}
finally {
H5F.close(fileId);
}
return(resultArray);
}
public void H5RdereferenceTest4()
{
byte[] path =
Encoding.UTF8.GetBytes(String.Join("/", m_utf8strings));
// make room for the trailling \0
byte[] name = new byte[path.Length + 1];
Array.Copy(path, name, path.Length);
hsize_t[] dims = new hsize_t[] { 10, 20 };
hid_t space = H5S.create_simple(2, dims, null);
Assert.IsTrue(space >= 0);
hid_t dset = H5D.create(m_v2_test_file, name, H5T.STD_I32LE, space,
m_lcpl_utf8);
H5O.info_t info = new H5O.info_t();
Assert.IsTrue(H5O.get_info(dset, ref info) >= 0);
haddr_t address = info.addr;
Assert.IsTrue(H5D.close(dset) >= 0);
Assert.IsTrue(dset >= 0);
hsize_t[] start = { 5, 10 };
hsize_t[] count = { 1, 1 };
hsize_t[] block = { 2, 4 };
Assert.IsTrue(
H5S.select_hyperslab(space, H5S.seloper_t.SET, start, null,
count, block) >= 0);
byte[] refer = new byte[H5R.DSET_REG_REF_BUF_SIZE];
GCHandle hnd = GCHandle.Alloc(refer, GCHandleType.Pinned);
Assert.IsTrue(
H5R.create(hnd.AddrOfPinnedObject(), m_v2_test_file, name,
H5R.type_t.DATASET_REGION, space) >= 0);
#if HDF5_VER1_10
dset = H5R.dereference(m_v2_test_file, H5P.DEFAULT,
H5R.type_t.DATASET_REGION, hnd.AddrOfPinnedObject());
#else
dset = H5R.dereference(m_v2_test_file, H5R.type_t.DATASET_REGION,
hnd.AddrOfPinnedObject());
#endif
Assert.IsTrue(dset >= 0);
hnd.Free();
Assert.IsTrue(H5O.get_info(dset, ref info) >= 0);
Assert.IsTrue(address == info.addr);
Assert.IsTrue(H5D.close(dset) >= 0);
Assert.IsTrue(H5S.close(space) >= 0);
}
public void H5Sget_select_hyper_nblocksTest1()
{
hsize_t[] dims = { 1, 2, 3 };
hid_t space = H5S.create_simple(dims.Length, dims, dims);
Assert.IsTrue(space > 0);
hsize_t[] start = { 0, 0, 0 };
hsize_t[] count = { 1, 1, 1 };
hsize_t[] block = { 1, 2, 3 };
Assert.IsTrue(
H5S.select_hyperslab(space, H5S.seloper_t.SET, start, null,
count, block) >= 0);
Assert.IsTrue(H5S.get_select_hyper_nblocks(space) == 1);
Assert.IsTrue(H5S.close(space) >= 0);
}
public static T[] ReadDataset <T>(long locationId, string datasetPath, ulong start = 0, ulong stride = 0, ulong block = 0, ulong count = 0)
{
long datasetId = -1;
long dataspaceId = -1;
T[] result;
try
{
datasetId = H5D.open(locationId, datasetPath);
if (H5I.is_valid(datasetId) <= 0)
{
throw new Exception(ErrorMessage.IOHelper_CouldNotOpenDataset);
}
if (start == 0 && stride == 0 && block == 0 && count == 0)
{
result = IOHelper.Read <T>(datasetId, DataContainerType.Dataset);
}
else
{
dataspaceId = H5D.get_space(datasetId);
if (H5S.select_hyperslab(dataspaceId, H5S.seloper_t.SET, new ulong[] { start }, new ulong[] { stride }, new ulong[] { block }, new ulong[] { count }) < 0)
{
throw new Exception(ErrorMessage.IOHelper_CouldNotSelectHyperslab);
}
result = IOHelper.Read <T>(datasetId, DataContainerType.Dataset, dataspaceId);
}
}
finally
{
if (H5I.is_valid(dataspaceId) > 0)
{
H5S.close(dataspaceId);
}
if (H5I.is_valid(datasetId) > 0)
{
H5D.close(datasetId);
}
}
return(result);
}
public static T[,] ReadDataset <T>(int groupId, string name, ulong beginIndex, ulong endIndex) where T : struct
{
ulong[] start = { 0, 0 }, stride = null, count = { 0, 0 },
block = null, offsetOut = new ulong[] { 0, 0 };
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);
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, maxDims);
start[0] = beginIndex;
start[1] = 0;
count[0] = endIndex - beginIndex;
count[1] = dims[1];
var status = H5S.select_hyperslab(spaceId, H5S.seloper_t.SET, start, stride, count, block);
// Define the memory dataspace.
T[,] dset = new T[count[0], count[1]];
var memId = H5S.create_simple(rank, count, null);
// Define memory hyperslab.
status = H5S.select_hyperslab(memId, H5S.seloper_t.SET, offsetOut, null,
count, null);
/*
* Read data from hyperslab in the file into the hyperslab in
* memory and display.
*/
GCHandle hnd = GCHandle.Alloc(dset, GCHandleType.Pinned);
H5D.read(datasetId, datatype, memId, spaceId,
H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
H5D.close(datasetId);
H5S.close(spaceId);
H5S.close(memId);
return(dset);
}
public void H5Soffset_simpleTest1()
{
hsize_t[] dims = { 10, 10 };
hid_t space = H5S.create_simple(dims.Length, dims, null);
Assert.IsTrue(space > 0);
hsize_t[] start = { 0, 0 };
hsize_t[] count = { 1, 1 };
hsize_t[] block = { 2, 3 };
Assert.IsTrue(
H5S.select_hyperslab(space, H5S.seloper_t.SET, start, null,
count, block) >= 0);
hssize_t[] offset = { 0, 0 };
Assert.IsTrue(H5S.offset_simple(space, offset) >= 0);
Assert.IsTrue(H5S.close(space) >= 0);
}
public void H5Rget_obj_typeTest3()
{
byte[] path =
Encoding.UTF8.GetBytes(String.Join("/", m_utf8strings));
// make room for the trailling \0
byte[] name = new byte[path.Length + 1];
Array.Copy(path, name, path.Length);
hsize_t[] dims = new hsize_t[] { 10, 20 };
hid_t space = H5S.create_simple(2, dims, null);
Assert.IsTrue(space >= 0);
hid_t dset = H5D.create(m_v0_test_file, name, H5T.STD_I32LE, space,
m_lcpl_utf8);
Assert.IsTrue(dset >= 0);
hsize_t[] start = { 5, 10 };
hsize_t[] count = { 1, 1 };
hsize_t[] block = { 2, 4 };
Assert.IsTrue(
H5S.select_hyperslab(space, H5S.seloper_t.SET, start, null,
count, block) >= 0);
byte[] refer = new byte[H5R.DSET_REG_REF_BUF_SIZE];
GCHandle hnd = GCHandle.Alloc(refer, GCHandleType.Pinned);
Assert.IsTrue(
H5R.create(hnd.AddrOfPinnedObject(), m_v0_test_file, name,
H5R.type_t.DATASET_REGION, space) >= 0);
H5O.type_t obj_type = H5O.type_t.UNKNOWN;
Assert.IsTrue(
H5R.get_obj_type(m_v0_test_file, H5R.type_t.DATASET_REGION,
hnd.AddrOfPinnedObject(), ref obj_type) >= 0);
hnd.Free();
Assert.IsTrue(obj_type == H5O.type_t.DATASET);
Assert.IsTrue(H5D.close(dset) >= 0);
Assert.IsTrue(H5S.close(space) >= 0);
}
public void AppendDataset(Array dataset)
{
if (!Hdf5Utils.GetRealName(GroupId, Datasetname, string.Empty).valid)
{
string msg = "call constructor or FirstDataset first before appending.";
Hdf5Utils.LogError?.Invoke(msg);
throw new Hdf5Exception(msg);
}
_oldDims = _currentDims;
_currentDims = GetDims(dataset);
int rank = dataset.Rank;
ulong[] zeros = Enumerable.Range(0, rank).Select(z => (ulong)0).ToArray();
/* Extend the dataset. Dataset becomes 10 x 3 */
var size = new[] { _oldDims[0] + _currentDims[0] }.Concat(_oldDims.Skip(1)).ToArray();
_status = H5D.set_extent(_datasetId, size);
ulong[] offset = new[] { _oldDims[0] }.Concat(zeros.Skip(1)).ToArray();
/* Select a hyperslab in extended portion of dataset */
var filespaceId = H5D.get_space(_datasetId);
_status = H5S.select_hyperslab(filespaceId, H5S.seloper_t.SET, offset, null,
_currentDims, null);
/* Define memory space */
var memId = H5S.create_simple(Rank, _currentDims, null);
/* Write the data to the extended portion of dataset */
GCHandle hnd = GCHandle.Alloc(dataset, GCHandleType.Pinned);
_status = H5D.write(_datasetId, _datatype, memId, filespaceId,
H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
_currentDims = size;
H5S.close(memId);
H5S.close(filespaceId);
}
public void H5Sselect_validTest1()
{
hsize_t[] dims = { 10, 20, 30 };
hid_t space = H5S.create_simple(dims.Length, dims, dims);
Assert.IsTrue(space > 0);
hsize_t[] start = { 0, 0, 0 };
hsize_t[] count = { 1, 1, 1 };
hsize_t[] block = { 1, 2, 3 };
Assert.IsTrue(
H5S.select_hyperslab(space, H5S.seloper_t.SET, start, null,
count, block) >= 0);
Assert.IsTrue(H5S.select_valid(space) > 0);
start[1] = 50;
Assert.IsTrue(
H5S.select_hyperslab(space, H5S.seloper_t.OR, start, null,
count, block) >= 0);
Assert.IsTrue(H5S.select_valid(space) == 0);
Assert.IsTrue(H5S.close(space) >= 0);
}
static void TestExtent(hid_t file, string dataSetName, ulong[] dims, ulong[] extent)
{
var dataSet = CreateDataSet(file, dataSetName, H5T.NATIVE_INT,
dims, new ulong[] { H5S.UNLIMITED, 4 }, new ulong[] { 4, 4 });
H5D.set_extent(dataSet, extent);
var fileSpace = H5D.get_space(dataSet);
H5S.select_hyperslab(fileSpace, H5S.seloper_t.SET,
new ulong[] { 0, 0 }, null, new ulong[] { 2, 4 }, null);
var memSpace = H5S.create_simple(2, new ulong[] { 2, 4 }, null);
if (H5D.write(dataSet, H5T.NATIVE_INT, memSpace, fileSpace, H5P.DEFAULT,
new PinnedObject(Enumerable.Range(0, 8).ToArray())) < 0)
{
WriteLine("H5D.write failed.");
}
H5D.close(dataSet);
}
public void AppendDataset(Array dataset)
{
if (!DatasetExists)
{
throw new Exception("call constructor or FirstDataset first before appending.");
}
oldDims = currentDims;
currentDims = getDims(dataset);
int rank = dataset.Rank;
ulong[] zeros = Enumerable.Range(0, rank).Select(z => (ulong)0).ToArray();
/* Extend the dataset. Dataset becomes 10 x 3 */
var size = new ulong[] { oldDims[0] + currentDims[0] }.Concat(oldDims.Skip(1)).ToArray();
status = H5D.set_extent(datasetId, size);
ulong[] offset = new ulong[] { oldDims[0] }.Concat(zeros.Skip(1)).ToArray();
/* Select a hyperslab in extended portion of dataset */
var filespaceId = H5D.get_space(datasetId);
status = H5S.select_hyperslab(filespaceId, H5S.seloper_t.SET, offset, null,
currentDims, null);
/* Define memory space */
var memId = H5S.create_simple(Rank, currentDims, null);
/* Write the data to the extended portion of dataset */
GCHandle hnd = GCHandle.Alloc(dataset, GCHandleType.Pinned);
status = H5D.write(datasetId, datatype, memId, filespaceId,
H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
currentDims = size;
H5S.close(memId);
//filespaceId must be closed by H5S.close() not H5D
H5S.close(filespaceId);
}
public static Array ReadDataset(long locationId, string datasetPath, ulong start = 0, ulong stride = 0, ulong block = 0, ulong count = 0)
{
long datasetId = -1;
long dataspaceId = -1;
long typeId = -1;
Array result;
try
{
datasetId = H5D.open(locationId, datasetPath);
if (H5I.is_valid(datasetId) <= 0)
{
throw new Exception(ErrorMessage.IOHelper_CouldNotOpenDataset);
}
typeId = H5D.get_type(datasetId);
if (start == 0 && stride == 0 && block == 0 && count == 0)
{
// invoke HdfHelper.Read
result = (Array)GeneralHelper.InvokeGenericMethod(typeof(IOHelper), null, nameof(IOHelper.Read),
BindingFlags.Public | BindingFlags.Static,
TypeConversionHelper.GetTypeFromHdfTypeId(typeId),
new object[] { datasetId, DataContainerType.Dataset, Type.Missing });
}
else
{
dataspaceId = H5D.get_space(datasetId);
if (H5S.select_hyperslab(dataspaceId, H5S.seloper_t.SET, new ulong[] { start }, new ulong[] { stride }, new ulong[] { count }, new ulong[] { block }) < 0)
{
throw new Exception(ErrorMessage.IOHelper_CouldNotSelectHyperslab);
}
// invoke HdfHelper.Read
result = (Array)GeneralHelper.InvokeGenericMethod(typeof(IOHelper), null, nameof(IOHelper.Read),
BindingFlags.Public | BindingFlags.Static,
TypeConversionHelper.GetTypeFromHdfTypeId(typeId),
new object[] { datasetId, DataContainerType.Dataset, dataspaceId });
}
}
finally
{
if (H5I.is_valid(dataspaceId) > 0)
{
H5S.close(dataspaceId);
}
if (H5I.is_valid(typeId) > 0)
{
H5T.close(typeId);
}
if (H5I.is_valid(datasetId) > 0)
{
H5D.close(datasetId);
}
}
return(result);
}
private static void createVDS()
{
// create files
m_a_class_file = Utilities.H5TempFile(ref m_a_class_file_name,
H5F.libver_t.LATEST, true);
Assert.IsTrue(m_a_class_file >= 0);
m_b_class_file = Utilities.H5TempFile(ref m_b_class_file_name,
H5F.libver_t.LATEST, true);
Assert.IsTrue(m_b_class_file >= 0);
m_c_class_file = Utilities.H5TempFile(ref m_c_class_file_name,
H5F.libver_t.LATEST, true);
Assert.IsTrue(m_c_class_file >= 0);
m_vds_class_file = Utilities.H5TempFile(ref m_vds_class_file_name);
Assert.IsTrue(m_vds_class_file >= 0);
//
// create target datasets
//
hid_t dcpl = H5P.create(H5P.DATASET_CREATE);
Assert.IsTrue(dcpl >= 0);
int fill_value = 1;
GCHandle hnd = GCHandle.Alloc(fill_value, GCHandleType.Pinned);
Assert.IsTrue(H5P.set_fill_value(dcpl, H5T.NATIVE_INT,
hnd.AddrOfPinnedObject()) >= 0);
hsize_t[] dims = { 6 };
hid_t src_dsp = H5S.create_simple(1, dims, null);
// A
fill_value = 1;
hid_t a = H5D.create(m_a_class_file, "A", H5T.STD_I32LE, src_dsp);
Assert.IsTrue(a >= 0);
Assert.IsTrue(H5D.close(a) >= 0);
// B
fill_value = 2;
hid_t b = H5D.create(m_b_class_file, "B", H5T.STD_I32LE, src_dsp);
Assert.IsTrue(b >= 0);
Assert.IsTrue(H5D.close(b) >= 0);
// B
fill_value = 3;
hid_t c = H5D.create(m_c_class_file, "C", H5T.STD_I32LE, src_dsp);
Assert.IsTrue(c >= 0);
Assert.IsTrue(H5D.close(c) >= 0);
//
// create the VDS
//
fill_value = -1;
hsize_t[] vds_dims = { 4, 6 };
hid_t vds_dsp = H5S.create_simple(2, vds_dims, null);
hsize_t[] start = { 0, 0 };
hsize_t[] count = { 1, 1 };
hsize_t[] block = { 1, 6 };
start[0] = 0;
Assert.IsTrue(H5S.select_hyperslab(vds_dsp, H5S.seloper_t.SET,
start, null, count, block) >= 0);
Assert.IsTrue(H5P.set_virtual(dcpl, vds_dsp,
m_a_class_file_name, "A", src_dsp) >= 0);
start[0] = 1;
Assert.IsTrue(H5S.select_hyperslab(vds_dsp, H5S.seloper_t.SET,
start, null, count, block) >= 0);
Assert.IsTrue(H5P.set_virtual(dcpl, vds_dsp,
m_b_class_file_name, "B", src_dsp) >= 0);
start[0] = 2;
Assert.IsTrue(H5S.select_hyperslab(vds_dsp, H5S.seloper_t.SET,
start, null, count, block) >= 0);
Assert.IsTrue(H5P.set_virtual(dcpl, vds_dsp,
m_c_class_file_name, "C", src_dsp) >= 0);
hid_t vds = H5D.create(m_vds_class_file, "VDS", H5T.STD_I32LE,
vds_dsp, H5P.DEFAULT, dcpl, H5P.DEFAULT);
Assert.IsTrue(vds >= 0);
Assert.IsTrue(H5D.close(vds) >= 0);
Assert.IsTrue(H5S.close(vds_dsp) >= 0);
Assert.IsTrue(H5S.close(src_dsp) >= 0);
Assert.IsTrue(H5P.close(dcpl) >= 0);
hnd.Free();
// close the satellite files
Assert.IsTrue(H5F.close(m_a_class_file) >= 0);
Assert.IsTrue(H5F.close(m_b_class_file) >= 0);
Assert.IsTrue(H5F.close(m_c_class_file) >= 0);
}
public void H5Sselect_hyperslabTest2()
{
Assert.IsFalse(
H5S.select_hyperslab(Utilities.RandomInvalidHandle(),
H5S.seloper_t.SET, (ulong[])null, null, null, null) >= 0);
}
/// <summary>
/// Appends a dataset to a hdf5 file. If called the first time a dataset is created
/// </summary>
/// <typeparam name="T">Generic parameter only primitive types are allowed</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 hid_t AppendDataset <T>(hid_t groupId, string name, Array dset, ulong chunkX = 200) where T : struct
{
var rank = dset.Rank;
ulong[] dimsExtend = Enumerable.Range(0, rank).Select(i =>
{ return((ulong)dset.GetLength(i)); }).ToArray();
ulong[] maxDimsExtend = null;
ulong[] dimsChunk = new ulong[] { chunkX }.Concat(dimsExtend.Skip(1)).ToArray();
ulong[] zeros = Enumerable.Range(0, rank).Select(z => (ulong)0).ToArray();
hid_t status, spaceId, datasetId;
// name = ToHdf5Name(name);
var datatype = GetDatatype(typeof(T));
var typeId = H5T.copy(datatype);
var datasetExists = H5L.exists(groupId, name) > 0;
/* Create a new dataset within the file using chunk
* creation properties. */
if (!datasetExists)
{
spaceId = H5S.create_simple(dset.Rank, dimsExtend, maxDimsExtend);
var propId = H5P.create(H5P.DATASET_CREATE);
status = H5P.set_chunk(propId, rank, dimsChunk);
datasetId = H5D.create(groupId, name, datatype, spaceId,
H5P.DEFAULT, propId, H5P.DEFAULT);
/* Write data to dataset */
GCHandle hnd = GCHandle.Alloc(dset, GCHandleType.Pinned);
status = H5D.write(datasetId, datatype, H5S.ALL, H5S.ALL, H5P.DEFAULT,
hnd.AddrOfPinnedObject());
hnd.Free();
H5P.close(propId);
}
else
{
datasetId = H5D.open(groupId, name);
spaceId = H5D.get_space(datasetId);
var rank_old = H5S.get_simple_extent_ndims(spaceId);
ulong[] maxDims = new ulong[rank_old];
ulong[] dims = new ulong[rank_old];
var memId1 = H5S.get_simple_extent_dims(spaceId, dims, maxDims);
ulong[] oldChunk = null;
int chunkDims = 0;
var propId = H5P.create(H5P.DATASET_ACCESS);
status = H5P.get_chunk(propId, chunkDims, oldChunk);
/* Extend the dataset. */
var size = new ulong[] { dims[0] + dimsExtend[0] }.Concat(dims.Skip(1)).ToArray();
status = H5D.set_extent(datasetId, size);
/* Select a hyperslab in extended portion of dataset */
var filespaceId = H5D.get_space(datasetId);
var offset = new ulong[] { dims[0] }.Concat(zeros.Skip(1)).ToArray();
status = H5S.select_hyperslab(filespaceId, H5S.seloper_t.SET, offset, null,
dimsExtend, null);
/* Define memory space */
var memId2 = H5S.create_simple(rank, dimsExtend, null);
/* Write the data to the extended portion of dataset */
GCHandle hnd = GCHandle.Alloc(dset, GCHandleType.Pinned);
status = H5D.write(datasetId, datatype, memId2, spaceId,
H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
H5S.close(memId1);
H5S.close(memId2);
H5D.close(filespaceId);
}
H5D.close(datasetId);
H5S.close(spaceId);
return(status);
}