public static (long DatasetId, bool IsNew) OpenOrCreateDataset(long locationId, string datasetPath, long datasetTypeId, ulong chunkLength, ulong chunkCount, IntPtr fillValue = default)
{
return(IOHelper.OpenOrCreateDataset(locationId, datasetPath, datasetTypeId, () =>
{
long dcPropertyId = -1;
long lcPropertyId = -1;
long dataspaceId = -1;
long datasetId = -1;
try
{
dcPropertyId = H5P.create(H5P.DATASET_CREATE);
if (fillValue != IntPtr.Zero)
{
H5P.set_fill_value(dcPropertyId, datasetTypeId, fillValue);
}
H5P.set_shuffle(dcPropertyId);
H5P.set_deflate(dcPropertyId, 7);
H5P.set_chunk(dcPropertyId, 1, new ulong[] { chunkLength });
lcPropertyId = H5P.create(H5P.LINK_CREATE);
H5P.set_create_intermediate_group(lcPropertyId, 1);
dataspaceId = H5S.create_simple(1, new ulong[] { chunkLength *chunkCount }, null);
datasetId = H5D.create(locationId, datasetPath, datasetTypeId, dataspaceId, lcPropertyId, dcPropertyId);
if (H5I.is_valid(datasetId) <= 0)
{
throw new Exception($"{ ErrorMessage.IOHelper_CouldNotOpenOrCreateDataset } Dataset: '{ datasetPath }'.");
}
}
finally
{
if (H5I.is_valid(dcPropertyId) > 0)
{
H5P.close(dcPropertyId);
}
if (H5I.is_valid(lcPropertyId) > 0)
{
H5P.close(lcPropertyId);
}
if (H5I.is_valid(dataspaceId) > 0)
{
H5S.close(dataspaceId);
}
}
return datasetId;
}));
}
public HDF5DataSet CreateDataset(string name, ulong[] shape, Type dType, long maxSize = 1,
bool[] unlimited = null, ulong[] chunkShape = null, bool compress = false)
{
HDF5DataSet result = null;
With((id) =>
{
int nDims = shape.Length;
if (unlimited == null)
{
unlimited = Enumerable.Range(0, nDims).Select(d => false).ToArray();
}
ulong[] maxShape =
Enumerable.Range(0, nDims).Select(d => unlimited[d] ? H5S.UNLIMITED : shape[d]).ToArray();
var dataspaceID = H5S.create_simple(nDims, shape, maxShape);
long dataTypeID = HDF5DataSet.OpenHDFDataType(dType, maxSize);
long creationPropertyList = 0L;
if (compress)
{
if (chunkShape == null)
{
chunkShape = shape;
}
creationPropertyList = H5P.create(H5P.DATASET_CREATE);
H5P.set_layout(creationPropertyList, H5D.layout_t.CHUNKED);
H5P.set_deflate(creationPropertyList, 9);
H5P.set_chunk(creationPropertyList, shape.Length, chunkShape);
}
var newID = H5D.create(id, name, dataTypeID, dataspaceID, 0L, creationPropertyList, 0L);
if (creationPropertyList > 0)
{
H5P.close(creationPropertyList);
}
H5T.close(dataTypeID);
H5S.close(dataspaceID);
if (newID <= 0)
{
throw new H5SSException("Couldn't create DataSet");
}
// write!
H5D.close(newID);
result = new HDF5DataSet(name, this);
});
return(result);
}
public static unsafe void AddChunkedDatasetForHyperslab(long fileId)
{
long res;
var dcpl_id = H5P.create(H5P.DATASET_CREATE);
var dims = new ulong[] { 25, 25, 4 };
var chunkDims = new ulong[] { 7, 20, 3 };
res = H5P.set_chunk(dcpl_id, 3, chunkDims);
TestUtils.Add(ContainerType.Dataset, fileId, "chunked", "hyperslab", H5T.NATIVE_INT32, TestData.MediumData.AsSpan(), dims, cpl: dcpl_id);
res = H5P.close(dcpl_id);
}
public static unsafe void AddFilteredDataset_ZLib(long fileId)
{
long res;
var length = (ulong)TestData.MediumData.Length / 4;
var dims = new ulong[] { length, 4 };
var dcpl_id = H5P.create(H5P.DATASET_CREATE);
res = H5P.set_chunk(dcpl_id, 2, new ulong[] { 1000, 4 });
res = H5P.set_filter(dcpl_id, H5Z.filter_t.DEFLATE, 0, new IntPtr(1), new uint[] { 5 } /* compression level */);
TestUtils.Add(ContainerType.Dataset, fileId, "filtered", $"deflate", H5T.NATIVE_INT32, TestData.MediumData.AsSpan(), dims, cpl: dcpl_id);
res = H5P.close(dcpl_id);
}
public static unsafe void AddChunkedDataset_Implicit(long fileId)
{
long res;
var length = (ulong)TestData.MediumData.Length / 4;
var dims = new ulong[] { length, 4 };
var dcpl_id = H5P.create(H5P.DATASET_CREATE);
res = H5P.set_chunk(dcpl_id, 2, new ulong[] { 1000, 3 });
res = H5P.set_alloc_time(dcpl_id, H5D.alloc_time_t.EARLY);
TestUtils.Add(ContainerType.Dataset, fileId, "chunked", "chunked_implicit", H5T.NATIVE_INT32, TestData.MediumData.AsSpan(), dims, cpl: dcpl_id);
res = H5P.close(dcpl_id);
}
public void H5DOappendTestSWMR1()
{
hsize_t[] dims = { 6, 0 };
hsize_t[] maxdims = { 6, H5S.UNLIMITED };
hsize_t[] chunk_dims = { 2, 5 };
int[] cbuf = new int [6];
hid_t dsp = H5S.create_simple(2, dims, maxdims);
Assert.IsTrue(dsp >= 0);
hid_t dcpl = H5P.create(H5P.DATASET_CREATE);
Assert.IsTrue(dcpl >= 0);
Assert.IsTrue(H5P.set_chunk(dcpl, 2, chunk_dims) >= 0);
hsize_t[] boundary = { 0, 1 };
hid_t dapl = H5P.create(H5P.DATASET_ACCESS);
Assert.IsTrue(dapl >= 0);
H5D.append_cb_t cb = DOappend_func;
Assert.IsTrue(
H5P.set_append_flush(dapl, 2, boundary, cb, new IntPtr(99)) >= 0);
hid_t dst = H5D.create(m_v3_test_file_swmr, "dset",
H5T.NATIVE_INT, dsp, H5P.DEFAULT, dcpl, dapl);
Assert.IsTrue(dst >= 0);
GCHandle hnd = GCHandle.Alloc(cbuf, GCHandleType.Pinned);
for (int i = 0; i < 3; ++i)
{
for (int j = 0; j < 6; ++j)
{
cbuf[j] = ((i * 6) + (j + 1)) * -1;
}
Assert.IsTrue(
H5DO.append(dst, H5P.DEFAULT, 1, new IntPtr(1),
H5T.NATIVE_INT, hnd.AddrOfPinnedObject()) >= 0);
}
hnd.Free();
Assert.IsTrue(H5D.close(dst) >= 0);
Assert.IsTrue(H5P.close(dapl) >= 0);
Assert.IsTrue(H5P.close(dcpl) >= 0);
Assert.IsTrue(H5S.close(dsp) >= 0);
}
public void AppendOrCreateDataset(Array dataset)
{
if (_chunkDims == null)
{
if (dataset.Rank < 1)
{
string msg = "Empty array was passed. Ignoring.";
Hdf5Utils.LogError?.Invoke(msg);
return;
}
for (int dimension = 1; dimension <= dataset.Rank; dimension++)
{
var size = dataset.GetUpperBound(dimension - 1) + 1;
if (size == 0)
{
string msg = $"Empty array was passed for dimension {dimension}. Ignoring.";
Hdf5Utils.LogError?.Invoke(msg);
return;
}
}
_chunkDims = new[]
{ Convert.ToUInt64(dataset.GetLongLength(0)), Convert.ToUInt64(dataset.GetLongLength(1)) };
Rank = dataset.Rank;
_currentDims = GetDims(dataset);
/* Create the data space with unlimited dimensions. */
_spaceId = H5S.create_simple(Rank, _currentDims, _maxDims);
/* Modify dataset creation properties, i.e. enable chunking */
_propId = H5P.create(H5P.DATASET_CREATE);
_status = H5P.set_chunk(_propId, Rank, _chunkDims);
/* Create a new dataset within the file using chunk creation properties. */
_datasetId = H5D.create(GroupId, Hdf5Utils.NormalizedName(Datasetname), _datatype, _spaceId, H5P.DEFAULT, _propId);
/* Write data to dataset */
GCHandle hnd = GCHandle.Alloc(dataset, GCHandleType.Pinned);
_status = H5D.write(_datasetId, _datatype, H5S.ALL, H5S.ALL, H5P.DEFAULT,
hnd.AddrOfPinnedObject());
hnd.Free();
H5S.close(_spaceId);
_spaceId = -1;
}
else
{
AppendDataset(dataset);
}
}
public static unsafe void AddFilteredDataset_Fletcher(long fileId)
{
long res;
var length = (ulong)TestData.MediumData.Length / 4;
var dims = new ulong[] { length, 4 };
var dcpl_id = H5P.create(H5P.DATASET_CREATE);
res = H5P.set_chunk(dcpl_id, 2, new ulong[] { 1000, 4 });
res = H5P.set_fletcher32(dcpl_id);
TestUtils.Add(ContainerType.Dataset, fileId, "filtered", $"fletcher", H5T.NATIVE_INT32, TestData.MediumData.AsSpan(), dims, cpl: dcpl_id);
res = H5P.close(dcpl_id);
}
/// <summary>
/// Create a new hdf5 `H5DataSet` at `loc_id`.
/// </summary>
/// <remarks>
/// `maxdims` may be `null` in which case it is set to `dims`.
/// </remarks>
internal static H5DataSet Create(hid_t loc_id, string key, int rank, long[] dims, long[] maxdims, Type primitive_type)
{
hid_t dcpl; // the 'dataset creation property list' controls chunking..
if (maxdims == null || dims.SequenceEqual(maxdims))
{
dcpl = H5P.DEFAULT;
}
else if (HasH5Pcreate)
{
// ..which is needed for later resizing:
var chunk = new ulong[rank];
// the chunk is of size 1 in each 'unlimited' dimension and of size 'maxdims'
// for all other dimensions (just like the 'SPECdata/Intensities' dataset):
for (int i = 0; i < rank; i++)
{
if (maxdims[i] == H5Space.Unlimited)
{
chunk[i] = 1UL;
}
else if (maxdims[i] > 0)
{
checked { chunk[i] = (ulong)maxdims[i]; }
}
else
{
throw new ArgumentException($"invalid value in parameter 'maxdims'");
}
}
dcpl = H5P.create(H5P.DATASET_CREATE);
H5P.set_chunk(dcpl, rank, chunk);
}
else
{
maxdims = dims;
dcpl = H5P.DEFAULT;
}
hid_t id;
using (H5Space space = H5Space.Create(rank, dims, maxdims))
using (H5Type dtype = H5Type.Create(primitive_type))
{
if ((id = H5D.create(loc_id, key, dtype.ID, space.ID, H5P.DEFAULT, dcpl, H5P.DEFAULT)) < 0)
{
throw new H5LibraryException($"H5D.create() returned ({id})");
}
}
return(FromID(id));
}
public void H5Dget_num_chunksTest1()
{
hsize_t[] dims = { 10, 10 };
hsize_t[] max_dims = { H5S.UNLIMITED, H5S.UNLIMITED };
hid_t space = H5S.create_simple(2, dims, max_dims);
hid_t dcpl = H5P.create(H5P.DATASET_CREATE);
Assert.IsTrue(dcpl >= 0);
hsize_t[] chunk = { 4, 4 };
Assert.IsTrue(H5P.set_chunk(dcpl, 2, chunk) >= 0);
Assert.IsTrue(H5P.set_alloc_time(dcpl, H5D.alloc_time_t.EARLY) >= 0);
Assert.IsTrue(H5P.set_fill_time(dcpl, H5D.fill_time_t.ALLOC) >= 0);
hid_t dset = H5D.create(m_v0_test_file, "Early Bird", H5T.IEEE_F32BE,
space, H5P.DEFAULT, dcpl);
Assert.IsTrue(dset >= 0);
// This should work but doesn't:
// Assert.IsTrue(H5D.get_num_chunks(dset, H5S.ALL, ref nchunks) >= 0);
hid_t fspace = H5D.get_space(dset);
Assert.IsTrue(fspace >= 0);
Assert.IsTrue(H5S.select_all(fspace) >= 0);
hsize_t nchunks = 0;
Assert.IsTrue(H5D.get_num_chunks(dset, fspace, ref nchunks) >= 0);
Assert.IsTrue(nchunks == 9);
Assert.IsTrue(H5D.close(dset) >= 0);
dset = H5D.create(m_v2_test_file, "Early Bird", H5T.IEEE_F32BE,
space, H5P.DEFAULT, dcpl);
Assert.IsTrue(dset >= 0);
// This should work but doesn't:
// Assert.IsTrue(H5D.get_num_chunks(dset, H5S.ALL, ref nchunks) >= 0);
fspace = H5D.get_space(dset);
Assert.IsTrue(fspace >= 0);
Assert.IsTrue(H5S.select_all(fspace) >= 0);
nchunks = 0;
Assert.IsTrue(H5D.get_num_chunks(dset, fspace, ref nchunks) >= 0);
Assert.IsTrue(nchunks == 9);
Assert.IsTrue(H5D.close(dset) >= 0);
}
public void H5Pset_chunk_optsTestSWMR1()
{
hid_t dcpl = H5P.create(H5P.DATASET_CREATE);
Assert.IsTrue(dcpl >= 0);
// without chunking, H5Pset_chunk_opts will throw an error
hsize_t[] dims = { 4711 };
Assert.IsTrue(H5P.set_chunk(dcpl, 1, dims) >= 0);
uint opts = H5D.DONT_FILTER_PARTIAL_CHUNKS;
Assert.IsTrue(H5P.set_chunk_opts(dcpl, opts) >= 0);
Assert.IsTrue(H5P.close(dcpl) >= 0);
}
public static void ClassInit(TestContext testContext)
{
#if HDF5_VER1_10
// create test files which persists across file tests
m_v3_class_file = Utilities.H5TempFileSWMR(ref m_v3_class_file_name);
Assert.IsTrue(m_v3_class_file >= 0);
m_lcpl = H5P.create(H5P.LINK_CREATE);
Assert.IsTrue(H5P.set_create_intermediate_group(m_lcpl, 1) >= 0);
m_lcpl_utf8 = H5P.copy(m_lcpl);
Assert.IsTrue(
H5P.set_char_encoding(m_lcpl_utf8, H5T.cset_t.UTF8) >= 0);
// create a sample dataset
hsize_t[] dims = { 6, 6 };
hsize_t[] maxdims = { 6, H5S.UNLIMITED };
hsize_t[] chunk_dims = { 2, 5 };
int[] cbuf = new int[36];
hid_t dsp = H5S.create_simple(2, dims, maxdims);
Assert.IsTrue(dsp >= 0);
hid_t dcpl = H5P.create(H5P.DATASET_CREATE);
Assert.IsTrue(dcpl >= 0);
Assert.IsTrue(H5P.set_chunk(dcpl, 2, chunk_dims) >= 0);
hid_t dst = H5D.create(m_v3_class_file, "int6x6",
H5T.NATIVE_INT, dsp, H5P.DEFAULT, dcpl);
Assert.IsTrue(dst >= 0);
GCHandle hnd = GCHandle.Alloc(cbuf, GCHandleType.Pinned);
Assert.IsTrue(H5D.write(dst, H5T.NATIVE_INT, H5S.ALL, H5S.ALL,
H5P.DEFAULT, hnd.AddrOfPinnedObject()) >= 0);
hnd.Free();
Assert.IsTrue(H5D.flush(dst) >= 0);
Assert.IsTrue(H5D.close(dst) >= 0);
Assert.IsTrue(H5P.close(dcpl) >= 0);
Assert.IsTrue(H5S.close(dsp) >= 0);
#endif
}
public static unsafe void AddChunkedDataset_Fixed_Array_Paged(long fileId, bool withShuffle)
{
long res;
var length = (ulong)TestData.MediumData.Length / 4;
var dims = new ulong[] { length, 4 };
var dcpl_id = H5P.create(H5P.DATASET_CREATE);
res = H5P.set_chunk(dcpl_id, 2, new ulong[] { 1, 3 });
if (withShuffle)
{
res = H5P.set_shuffle(dcpl_id);
}
TestUtils.Add(ContainerType.Dataset, fileId, "chunked", "chunked_fixed_array_paged", H5T.NATIVE_INT32, TestData.MediumData.AsSpan(), dims, cpl: dcpl_id);
res = H5P.close(dcpl_id);
}
public static unsafe void AddChunkedDatasetWithFillValueAndAllocationLate(long fileId, int fillValue)
{
long res;
var length = (ulong)TestData.MediumData.Length;
var dcpl_id = H5P.create(H5P.DATASET_CREATE);
res = H5P.set_alloc_time(dcpl_id, H5D.alloc_time_t.LATE);
res = H5P.set_chunk(dcpl_id, 1, new ulong[] { 1000 });
var handle = GCHandle.Alloc(BitConverter.GetBytes(fillValue), GCHandleType.Pinned);
H5P.set_fill_value(dcpl_id, H5T.NATIVE_INT, handle.AddrOfPinnedObject());
handle.Free();
TestUtils.Add(ContainerType.Dataset, fileId, "fillvalue", $"{LayoutClass.Chunked}", H5T.NATIVE_INT32, (void *)0, length, cpl: dcpl_id);
res = H5P.close(dcpl_id);
}
public void H5PglobalsTest1()
{
hsize_t[] dims = { 10, 10, 10 };
hsize_t[] max_dims = { H5S.UNLIMITED, H5S.UNLIMITED, H5S.UNLIMITED };
hid_t space = H5S.create_simple(3, dims, max_dims);
hid_t lcpl = H5P.create(H5P.LINK_CREATE);
Assert.IsTrue(H5P.set_create_intermediate_group(lcpl, 1) >= 0);
hid_t dcpl = H5P.create(H5P.DATASET_CREATE);
Assert.IsTrue(dcpl >= 0);
hsize_t[] chunk = { 64, 64, 64 };
Assert.IsTrue(H5P.set_chunk(dcpl, 3, chunk) >= 0);
Assert.IsTrue(H5P.set_deflate(dcpl, 9) >= 0);
hid_t dset = H5D.create(m_v0_test_file, "A/B/C", H5T.IEEE_F32BE,
space, lcpl, dcpl);
Assert.IsTrue(dset >= 0);
hid_t plist = H5D.get_create_plist(dset);
Assert.IsTrue(H5D.layout_t.CHUNKED == H5P.get_layout(plist));
Assert.IsTrue(H5P.close(plist) >= 0);
Assert.IsTrue(H5D.close(dset) >= 0);
dset = H5D.create(m_v2_test_file, "A/B/C", H5T.IEEE_F32BE,
space, lcpl, dcpl);
Assert.IsTrue(dset >= 0);
plist = H5D.get_create_plist(dset);
Assert.IsTrue(H5D.layout_t.CHUNKED == H5P.get_layout(plist));
Assert.IsTrue(H5P.close(plist) >= 0);
Assert.IsTrue(H5D.close(dset) >= 0);
Assert.IsTrue(H5P.close(dcpl) >= 0);
Assert.IsTrue(H5P.close(lcpl) >= 0);
Assert.IsTrue(H5S.close(space) >= 0);
}
public static unsafe void AddChunkedDataset_Extensible_Array_Secondary_Blocks(long fileId, bool withShuffle)
{
long res;
var length = (ulong)TestData.MediumData.Length / 4;
var dims0 = new ulong[] { length, 4 };
var dims1 = new ulong[] { H5S.UNLIMITED, 4 };
var dcpl_id = H5P.create(H5P.DATASET_CREATE);
res = H5P.set_chunk(dcpl_id, 2, new ulong[] { 3, 3 });
if (withShuffle)
{
res = H5P.set_shuffle(dcpl_id);
}
TestUtils.Add(ContainerType.Dataset, fileId, "chunked", "chunked_extensible_array_secondary_blocks", H5T.NATIVE_INT32, TestData.MediumData.AsSpan(), dims0, dims1, cpl: dcpl_id);
res = H5P.close(dcpl_id);
}
public static unsafe void AddChunkedDataset_BTree2(long fileId, bool withShuffle)
{
long res;
var length = (ulong)TestData.MediumData.Length / 4;
var dims0 = new ulong[] { length, 4 };
var dims1 = new ulong[] { H5S.UNLIMITED, H5S.UNLIMITED };
var dcpl_id = H5P.create(H5P.DATASET_CREATE);
res = H5P.set_chunk(dcpl_id, 2, new ulong[] { 1000, 3 });
if (withShuffle)
{
res = H5P.set_shuffle(dcpl_id);
}
TestUtils.Add(ContainerType.Dataset, fileId, "chunked", "chunked_btree2", H5T.NATIVE_INT32, TestData.MediumData.AsSpan(), dims0, dims1, cpl: dcpl_id);
res = H5P.close(dcpl_id);
}
public static unsafe void AddFilteredDataset_Shuffle(long fileId, int bytesOfType, int length, Span <byte> dataset)
{
long res;
var dcpl_id = H5P.create(H5P.DATASET_CREATE);
res = H5P.set_chunk(dcpl_id, 1, new ulong[] { (ulong)length });
res = H5P.set_shuffle(dcpl_id);
var typeId = bytesOfType switch
{
1 => H5T.NATIVE_UINT8,
2 => H5T.NATIVE_UINT16,
4 => H5T.NATIVE_UINT32,
8 => H5T.NATIVE_UINT64,
_ => throw new Exception($"The value '{bytesOfType}' of the 'bytesOfType' parameter is not within the valid range.")
};
TestUtils.Add(ContainerType.Dataset, fileId, "filtered", $"shuffle_{bytesOfType}", typeId, dataset, (ulong)length, cpl: dcpl_id);
res = H5P.close(dcpl_id);
}
public void H5Dget_chunk_info_by_coordTest2()
{
hsize_t[] dims = { 10, 10 };
hsize_t[] max_dims = { H5S.UNLIMITED, H5S.UNLIMITED };
hid_t space = H5S.create_simple(2, dims, max_dims);
hid_t dcpl = H5P.create(H5P.DATASET_CREATE);
Assert.IsTrue(dcpl >= 0);
hsize_t[] chunk = { 4, 4 };
Assert.IsTrue(H5P.set_chunk(dcpl, 2, chunk) >= 0);
hid_t dset = H5D.create(m_v0_test_file, "Early Bird3", H5T.IEEE_F32BE,
space, H5P.DEFAULT, dcpl);
Assert.IsTrue(dset >= 0);
hsize_t size = 100;
hsize_t[] offset = { 1, 2 };
uint32_t filter_mask = 0;
haddr_t addr = 0;
Assert.IsTrue(H5D.get_chunk_info_by_coord(dset, offset, ref filter_mask, ref addr, ref size) >= 0);
Assert.IsTrue(filter_mask == 0 && size == 0 && addr == H5.HADDR_UNDEF);
Assert.IsTrue(H5D.close(dset) >= 0);
dset = H5D.create(m_v2_test_file, "Early Bird3", H5T.IEEE_F32BE,
space, H5P.DEFAULT, dcpl);
Assert.IsTrue(dset >= 0);
size = 100;
addr = 0;
Assert.IsTrue(H5D.get_chunk_info_by_coord(dset, offset, ref filter_mask, ref addr, ref size) >= 0);
Assert.IsTrue(filter_mask == 0 && size == 0 && addr == H5.HADDR_UNDEF);
Assert.IsTrue(H5D.close(dset) >= 0);
}
public void FirstDataset(Array dataset)
{
if (GroupId <= 0)
{
throw new Hdf5Exception("cannot call FirstDataset because group or file couldn't be created");
}
if (Hdf5Utils.GetRealName(GroupId, Datasetname, string.Empty).valid)
{
throw new Hdf5Exception("cannot call FirstDataset because dataset already exists");
}
Rank = dataset.Rank;
_currentDims = GetDims(dataset);
/* Create the data space with unlimited dimensions. */
_spaceId = H5S.create_simple(Rank, _currentDims, _maxDims);
/* Modify dataset creation properties, i.e. enable chunking */
_propId = H5P.create(H5P.DATASET_CREATE);
_status = H5P.set_chunk(_propId, Rank, _chunkDims);
/* Create a new dataset within the file using chunk creation properties. */
_datasetId = H5D.create(GroupId, Hdf5Utils.NormalizedName(Datasetname), _datatype, _spaceId, H5P.DEFAULT, _propId);
/* Write data to dataset */
GCHandle hnd = GCHandle.Alloc(dataset, GCHandleType.Pinned);
_status = H5D.write(_datasetId, _datatype, H5S.ALL, H5S.ALL, H5P.DEFAULT,
hnd.AddrOfPinnedObject());
if (_status < 0)
{
Hdf5Utils.LogError("Unable to write dataset");
}
hnd.Free();
H5S.close(_spaceId);
_spaceId = -1;
}
public static Hdf5Dataset CreateDataset(
Hdf5Identifier _fileId,
Hdf5Path _parentPath,
string _name,
Hdf5DataTypes _datatype,
int _numberOfDimensions,
List <Hdf5DimensionProperty> _properties,
Hdf5CompressionProperty _compressionProperty = null)
{
Hdf5Path path = _parentPath.Append(_name);
UInt64[] dimensionSize = new UInt64[_numberOfDimensions];
UInt64[] maxSize = null; // new UInt64[_numberOfDimensions];
if (_numberOfDimensions != _properties.Count ||
(_compressionProperty != null && _numberOfDimensions != _compressionProperty.ChunkDimensions.Length))
{
throw new Hdf5ArrayDimensionsMismatchException();
}
int i = 0;
foreach (var property in _properties)
{
dimensionSize[i] = property.CurrentSize;
if (_compressionProperty != null && _compressionProperty.ChunkDimensions[i] > property.CurrentSize)
{
throw new Hdf5ArraySizeMismatchException();
}
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);
var plist_id = _compressionProperty != null?H5P.create(H5P.DATASET_CREATE) : 0;
if (plist_id != 0)
{
H5P.set_chunk(plist_id, _compressionProperty.ChunkDimensions.Length, _compressionProperty.ChunkDimensions);
H5P.set_deflate(plist_id, _compressionProperty.CompressionLevel);
}
Hdf5Identifier datasetId = H5D.create(_fileId.Value, path.FullPath, typeId.Value, dataspaceId.Value, dcpl_id: plist_id).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);
if (plist_id != 0)
{
H5P.close(plist_id);
}
FileHelper.FlushToFile(_fileId);
return(dataset);
}
public static hid_t CreateDataSet(hid_t hid, string dataSetName, hid_t typeId, ulong[] dims, ulong[] maxDims = null, ulong[] chunk = null, object fillValue = null)
{
if (string.IsNullOrEmpty(dataSetName))
{
throw new ArgumentException("dataSetName");
}
if (dims == null)
{
throw new ArgumentNullException("dims");
}
if (maxDims != null && maxDims.Length != dims.Length)
{
throw new ArgumentException("dims and maxDims should have the identical length.");
}
var chunked = false;
if (maxDims != null)
{
for (int i = 0; i < dims.Length; ++i)
{
if (maxDims[i] != H5S.UNLIMITED && maxDims[i] < dims[i])
{
throw new ArgumentException("maxDims[i] < dims[i]");
}
if (!chunked)
{
chunked = maxDims[i] == H5S.UNLIMITED;
}
}
}
if (chunked)
{
if (chunk == null)
{
throw new ArgumentNullException("chunk");
}
if (chunk.Length != dims.Length)
{
throw new ArgumentException("chunk");
}
if (chunk.Any(size => size <= 0))
{
throw new ArgumentException("All dimensions should have a positive length.");
}
}
if (DataSetExists(hid, dataSetName))
{
throw new HDF5Exception("Data set \"{0}\" already exists.", dataSetName);
}
var space = H5S.create_simple(dims.Length, dims, maxDims);
if (space < 0)
{
throw new HDF5Exception("H5S.create_simple failed.");
}
if (!chunked)
{
var dataSet = H5D.create(hid, dataSetName, typeId, space);
H5S.close(space);
if (dataSet < 0)
{
throw new HDF5Exception("Failed to create data set \"{0}\".", dataSetName);
}
return(dataSet);
}
else
{
var createPropertyList = H5P.create(H5P.DATASET_CREATE);
if (createPropertyList < 0)
{
H5S.close(space);
throw new HDF5Exception("Failed to create property list for chunked data set \"{0}\".", dataSetName);
}
if (H5P.set_chunk(createPropertyList, chunk.Length, chunk) < 0)
{
H5S.close(space);
throw new HDF5Exception("H5P.set_chunk failed.");
}
var dataSet = H5D.create(hid, dataSetName, typeId, space, H5P.DEFAULT, createPropertyList, H5P.DEFAULT);
H5S.close(space);
H5P.close(createPropertyList);
if (dataSet < 0)
{
throw new HDF5Exception("Failed to create chunked data set \"{0}\".", dataSetName);
}
return(dataSet);
}
}
/// <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);
}
