public void H5DflushTestSWMR2()
{
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_test_file_swmr, "dset",
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);
}
public void H5Dget_storage_sizeTest1()
{
hsize_t[] dims = { 1024, 2048 };
hid_t space = H5S.create_simple(2, dims, null);
hid_t dcpl = H5P.create(H5P.DATASET_CREATE);
Assert.IsTrue(dcpl >= 0);
Assert.IsTrue(
H5P.set_alloc_time(dcpl, H5D.alloc_time_t.EARLY) >= 0);
hid_t dset = H5D.create(m_v0_test_file, "dset", H5T.STD_I16LE,
space, H5P.DEFAULT, dcpl);
Assert.IsTrue(dset >= 0);
Assert.IsTrue(H5D.get_storage_size(dset) == 4194304);
Assert.IsTrue(H5D.close(dset) >= 0);
dset = H5D.create(m_v2_test_file, "dset", H5T.STD_I16LE,
space, H5P.DEFAULT, dcpl);
Assert.IsTrue(dset >= 0);
Assert.IsTrue(H5D.get_storage_size(dset) == 4194304);
Assert.IsTrue(H5D.close(dset) >= 0);
Assert.IsTrue(H5P.close(dcpl) >= 0);
Assert.IsTrue(H5S.close(space) >= 0);
}
public void AppendOrCreateDataset(Array dataset)
{
if (_chunkDims == null)
{
_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 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 H5DcreateTest2()
{
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);
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);
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 void H5Dget_typeTest1()
{
hsize_t[] dims = { 1024, 2048 };
hid_t space = H5S.create_simple(3, dims, null);
hid_t dset = H5D.create(m_v0_test_file, "dset", H5T.STD_I16LE,
space);
Assert.IsTrue(dset >= 0);
hid_t type = H5D.get_type(dset);
Assert.IsTrue(type >= 0);
Assert.IsTrue(H5T.equal(type, H5T.STD_I16LE) > 0);
Assert.IsTrue(H5T.close(type) >= 0);
Assert.IsTrue(H5D.close(dset) >= 0);
dset = H5D.create(m_v2_test_file, "dset", H5T.STD_I16LE,
space);
Assert.IsTrue(dset >= 0);
type = H5D.get_type(dset);
Assert.IsTrue(type >= 0);
Assert.IsTrue(H5T.equal(type, H5T.STD_I16LE) > 0);
Assert.IsTrue(H5T.close(type) >= 0);
Assert.IsTrue(H5D.close(dset) >= 0);
Assert.IsTrue(H5S.close(space) >= 0);
}
// information: https://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/hdf5-examples/1_8/C/H5T/h5ex_t_cmpd.c
//or: https://www.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html#t=HDF5_Users_Guide%2FDatatypes%2FHDF5_Datatypes.htm%3Frhtocid%3Dtoc6.5%23TOC_6_8_Complex_Combinationsbc-22
public static int WriteCompounds <T>(hid_t groupId, string name, IEnumerable <T> list) //where T : struct
{
Type type = typeof(T);
var size = Marshal.SizeOf(type);
var cnt = list.Count();
var typeId = create_type(type);
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[] { c_s };
ulong[] dims = new ulong[] { (ulong)cnt };
long dcpl = 0;
if (list.Count() == 0 || log10 == 0)
{
}
else
{
dcpl = create_property(chunk_size);
}
// Create dataspace. Setting maximum size to NULL sets the maximum
// size to be the current size.
var spaceId = H5S.create_simple(dims.Length, dims, null);
// Create the dataset and write the compound data to it.
var datasetId = H5D.create(groupId, name, typeId, spaceId, H5P.DEFAULT, dcpl);
IntPtr p = Marshal.AllocHGlobal(size * (int)dims[0]);
var ms = new MemoryStream();
BinaryWriter writer = new BinaryWriter(ms);
foreach (var strct in list)
{
writer.Write(getBytes(strct));
}
var bytes = ms.ToArray();
GCHandle hnd = GCHandle.Alloc(bytes, GCHandleType.Pinned);
var statusId = H5D.write(datasetId, typeId, spaceId, H5S.ALL,
H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
/*
* Close and release resources.
*/
H5D.close(datasetId);
H5S.close(spaceId);
H5T.close(typeId);
H5P.close(dcpl);
Marshal.FreeHGlobal(p);
return(statusId);
}
private void Write(H5GroupId parent, string name, IEnumerable <IMeasurement> measurements)
{
H5DataSpaceId spaceId = H5S.create_simple(1, new long[1] {
(long)measurements.Count()
});
// Set compression options for dataset
H5PropertyListId dataSetPropertyList = H5P.create(H5P.PropertyListClass.DATASET_CREATE);
H5P.setDeflate(dataSetPropertyList, NumericDataCompression);
H5P.setChunk(dataSetPropertyList, new long[] { (long)measurements.Count() });
H5DataSetId dataSetId = H5D.create(parent,
name,
measurement_t,
spaceId,
new H5PropertyListId(H5P.Template.DEFAULT),
dataSetPropertyList,
new H5PropertyListId(H5P.Template.DEFAULT));
MeasurementT[] ms = new MeasurementT[measurements.Count()];
int ilmCount = 0;
foreach (IMeasurement m in measurements)
{
MeasurementT mt = Convert(m);
ms[ilmCount++] = mt;
}
H5D.write <MeasurementT>(dataSetId, measurement_t, new H5Array <MeasurementT>(ms));
H5D.close(dataSetId);
H5S.close(spaceId);
}
public void FirstDataset(Array dataset)
{
if (FalseGroupId)
{
throw new Exception("cannot call FirstDataset because group or file couldn't be created");
}
if (DatasetExists)
{
throw new Exception("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, Datasetname, datatype, spaceId, H5P.DEFAULT, propId, H5P.DEFAULT);
/* 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);
}
private static long GetId(long parentId, string name, long dataType, long spaceId, Hdf5ElementType type)
{
string normalizedName = NormalizedName(name);
bool exists = ItemExists(parentId, normalizedName, type);
if (exists)
{
LogMessage($"{normalizedName} already exists", Hdf5LogLevel.Debug);
if (!Hdf5.Settings.OverrideExistingData)
{
if (Hdf5.Settings.ThrowOnError)
{
throw new Hdf5Exception($"{normalizedName} already exists");
}
return(-1);
}
}
var datasetId = -1L;
switch (type)
{
case Hdf5ElementType.Unknown:
break;
case Hdf5ElementType.Group:
case Hdf5ElementType.Dataset:
if (exists)
{
H5L.delete(parentId, normalizedName);
// datasetId = H5D.open(parentId, normalizedName);
}
datasetId = H5D.create(parentId, normalizedName, dataType, spaceId);
break;
case Hdf5ElementType.Attribute:
if (exists)
{
H5A.delete(parentId, normalizedName);
}
datasetId = H5A.create(parentId, normalizedName, dataType, spaceId);
break;
default:
throw new ArgumentOutOfRangeException(nameof(type), type, null);
}
if (datasetId == -1L)
{
string error = $"Unable to create dataset for {normalizedName}";
LogMessage($"{normalizedName} already exists", Hdf5LogLevel.Error);
if (Hdf5.Settings.ThrowOnError)
{
throw new Hdf5Exception(error);
}
}
return(datasetId);
}
public static unsafe void AddSomeLinks(long fileId)
{
long res;
var groupId = H5G.create(fileId, "simple");
var groupId_sub = H5G.create(groupId, "sub");
// datasets
var dataspaceId1 = H5S.create_simple(1, new ulong[] { 1 }, new ulong[] { 1 });
var datasetId1 = H5D.create(fileId, "D", H5T.NATIVE_INT8, dataspaceId1);
var data1 = new byte[] { 1 };
fixed(void *ptr = data1)
{
res = H5D.write(datasetId1, H5T.NATIVE_INT8, dataspaceId1, dataspaceId1, 0, new IntPtr(ptr));
}
res = H5D.close(datasetId1);
res = H5S.close(dataspaceId1);
var dataspaceId2 = H5S.create_simple(1, new ulong[] { 1 }, new ulong[] { 1 });
var datasetId2 = H5D.create(groupId, "D1", H5T.NATIVE_INT8, dataspaceId2);
res = H5D.close(datasetId2);
res = H5S.close(dataspaceId2);
var dataspaceId3 = H5S.create_simple(1, new ulong[] { 1 }, new ulong[] { 1 });
var datasetId3 = H5D.create(groupId_sub, "D1.1", H5T.NATIVE_INT8, dataspaceId3);
res = H5D.close(datasetId3);
res = H5S.close(dataspaceId3);
res = H5G.close(groupId);
res = H5G.close(groupId_sub);
}
public void H5DwriteTest1()
{
string utf8string
= "Γαζέες καὶ μυρτιὲς δὲν θὰ βρῶ πιὰ στὸ χρυσαφὶ ξέφωτο";
byte[] wdata = Encoding.UTF8.GetBytes(utf8string);
hid_t dtype = H5T.create(H5T.class_t.STRING,
new IntPtr(wdata.Length));
Assert.IsTrue(H5T.set_cset(dtype, H5T.cset_t.UTF8) >= 0);
Assert.IsTrue(H5T.set_strpad(dtype, H5T.str_t.SPACEPAD) >= 0);
hid_t dset_v0 = H5D.create(m_v0_test_file, "dset", dtype,
m_space_scalar);
Assert.IsTrue(dset_v0 >= 0);
hid_t dset_v2 = H5D.create(m_v2_test_file, "dset", dtype,
m_space_scalar);
Assert.IsTrue(dset_v2 >= 0);
GCHandle hnd = GCHandle.Alloc(wdata, GCHandleType.Pinned);
Assert.IsTrue(H5D.write(dset_v0, dtype, H5S.ALL,
H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject()) >= 0);
Assert.IsTrue(H5D.write(dset_v2, dtype, H5S.ALL,
H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject()) >= 0);
hnd.Free();
Assert.IsTrue(H5T.close(dtype) >= 0);
Assert.IsTrue(H5D.close(dset_v2) >= 0);
Assert.IsTrue(H5D.close(dset_v0) >= 0);
}
public void H5Dget_spaceTest1()
{
hsize_t[] dims = { 1024, 2048 };
hid_t space = H5S.create_simple(3, dims, null);
hid_t dset = H5D.create(m_v0_test_file, "dset", H5T.STD_I16LE,
space);
Assert.IsTrue(dset >= 0);
hid_t space1 = H5D.get_space(dset);
Assert.IsTrue(space1 >= 0);
Assert.IsTrue(H5S.extent_equal(space, space1) > 0);
Assert.IsTrue(H5S.close(space1) >= 0);
Assert.IsTrue(H5D.close(dset) >= 0);
dset = H5D.create(m_v2_test_file, "dset", H5T.STD_I16LE,
space);
Assert.IsTrue(dset >= 0);
space1 = H5D.get_space(dset);
Assert.IsTrue(space1 >= 0);
Assert.IsTrue(H5S.extent_equal(space, space1) > 0);
Assert.IsTrue(H5S.close(space1) >= 0);
Assert.IsTrue(H5D.close(dset) >= 0);
Assert.IsTrue(H5S.close(space) >= 0);
}
public void H5DOappendTestSWMR2()
{
hsize_t[] dims = { 0 };
hsize_t[] maxdims = { H5S.UNLIMITED };
hsize_t[] chunk_dims = { 10 };
uint[] cbuf = { 123, 456, 789 };
hid_t dsp = H5S.create_simple(1, dims, maxdims);
Assert.IsTrue(dsp >= 0);
hid_t dcpl = H5P.create(H5P.DATASET_CREATE);
Assert.IsTrue(dcpl >= 0);
Assert.IsTrue(H5P.set_chunk(dcpl, 1, chunk_dims) >= 0);
hid_t dst = H5D.create(m_v3_test_file_no_swmr, "dset1",
H5T.NATIVE_UINT, dsp, H5P.DEFAULT, dcpl, H5P.DEFAULT);
Assert.IsTrue(dst >= 0);
GCHandle hnd = GCHandle.Alloc(cbuf, GCHandleType.Pinned);
Assert.IsTrue(
H5DO.append(dst, H5P.DEFAULT, 0, new IntPtr(3),
H5T.NATIVE_UINT, hnd.AddrOfPinnedObject()) >= 0);
hnd.Free();
Assert.IsTrue(H5D.close(dst) >= 0);
Assert.IsTrue(H5P.close(dcpl) >= 0);
Assert.IsTrue(H5S.close(dsp) >= 0);
}
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);
}
private static void WriteFile(string filePath)
{
var file = H5F.create(filePath, H5F.CreateMode.ACC_TRUNC);
var group = H5G.create(file, "/group");
H5G.close(group);
const int RANK = 2;
const int DIM0 = 3;
const int DIM1 = 4;
var dims = new long[RANK] {
DIM0, DIM1
};
var dataSpace = H5S.create_simple(RANK, dims);
var dataSet = H5D.create(file, "/group/dataset", H5T.H5Type.NATIVE_INT, dataSpace);
H5S.close(dataSpace);
var data = new int[DIM0, DIM1]
{
{ 1, 2, 3, 4 },
{ 5, 6, 7, 8 },
{ 9, 10, 11, 12 }
};
H5D.write(dataSet, new H5DataTypeId(H5T.H5Type.NATIVE_INT), new H5Array <int>(data));
var dataType = new H5DataTypeId(H5T.H5Type.NATIVE_INT);
dataSpace = H5S.create(H5S.H5SClass.SCALAR);
var integerAttribute = H5A.create(dataSet, "int", dataType, dataSpace);
H5A.write(integerAttribute, dataType, new H5Array <int>(new int[1] {
42
}));
H5A.close(integerAttribute);
H5S.close(dataSpace);
//H5T.close(dataType); // Read-only.
var str = "Hello, world!";
var strBytes = Encoding.ASCII.GetBytes(str);
// There is a H5T.get_cset, but there does not seem to be a way of setting the character encoding, i.e. set_cset.
dataType = H5T.copy(H5T.H5Type.C_S1);
H5T.setSize(dataType, strBytes.Length);
dataSpace = H5S.create(H5S.H5SClass.SCALAR);
var stringAttribute = H5A.create(dataSet, "string", dataType, dataSpace);
H5A.write(stringAttribute, dataType, new H5Array <byte>(strBytes));
H5A.close(stringAttribute);
H5S.close(dataSpace);
H5T.close(dataType);
H5D.close(dataSet);
H5F.close(file);
}
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);
}
static void test_file_open()
{
try
{
// Output message about test being performed.
Console.Write("Testing file opening I/O");
// First ensure the file does not exist
File.Delete(FILE2);
// Try opening a non-existent file. This should fail.
try
{
H5FileId non_exist_file = H5F.open(FILE2, H5F.OpenMode.ACC_RDWR);
// should fail, but didn't, print out the error message.
Console.WriteLine("\ntest_file_open: Attempting to open a non-existent file.");
nerrors++;
}
catch (H5FopenException) { } // does nothing, it should fail
// Open the file.
H5FileId fileId = H5F.open(FILE1, H5F.OpenMode.ACC_RDWR);
// Create dataspace for the dataset in the file.
hssize_t[] dims = { 20 };
H5DataSpaceId dspace = H5S.create_simple(RANK, dims);
// Create a group.
H5GroupId groupId = H5G.create(fileId, GROUP_NAME);
// Create a dataset using file as location.
H5DataSetId dset1Id = H5D.create(fileId, DSET1_NAME, H5T.H5Type.NATIVE_INT, dspace);
// Create a dataset using group as location.
H5DataSetId dset2Id = H5D.create(groupId, DSET2_NAME, H5T.H5Type.NATIVE_SHORT, dspace);
// Close objects and files.
H5D.close(dset1Id);
H5D.close(dset2Id);
H5S.close(dspace);
H5G.close(groupId);
H5F.close(fileId);
Console.WriteLine("\t\t\t\tPASSED");
}
catch (HDFException anyHDF5E)
{
Console.WriteLine(anyHDF5E.Message);
nerrors++;
}
catch (System.Exception sysE)
{
Console.WriteLine(sysE.TargetSite);
Console.WriteLine(sysE.Message);
nerrors++;
}
} // test_file_open
public static Hdf5Dataset CreateDataset(
Hdf5Identifier _fileId,
Hdf5Path _parentPath,
string _name,
Hdf5DataTypes _datatype,
int _numberOfDimensions,
List <Hdf5DimensionProperty> _properties)
{
Hdf5Path path = _parentPath.Append(_name);
UInt64[] dimensionSize = new UInt64[_numberOfDimensions];
UInt64[] maxSize = null; // new UInt64[_numberOfDimensions];
int i = 0;
foreach (var property in _properties)
{
dimensionSize[i] = property.CurrentSize;
//if (property.MaximumSize == UInt64.MaxValue)
//{
// maxSize[i] = H5S.UNLIMITED;
//}
//else
//{
// maxSize[i] = property.MaximumSize;
//}
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);
Hdf5Identifier datasetId = H5D.create(_fileId.Value, path.FullPath, typeId.Value, dataspaceId.Value).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);
FileHelper.FlushToFile(_fileId);
return(dataset);
}
public void H5Dget_chunk_infoTest1()
{
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 Bird1", 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 index = 8, size = 0;
hsize_t[] offset = { 4711, 4712 };
uint32_t filter_mask = 0;
haddr_t addr = 0;
Assert.IsTrue(H5D.get_chunk_info(dset, fspace, index, offset, ref filter_mask, ref addr, ref size) >= 0);
Assert.IsTrue(offset[0] > 0);
Assert.IsTrue(filter_mask == 0 && size > 0 && addr > 0);
Assert.IsTrue(H5D.close(dset) >= 0);
dset = H5D.create(m_v2_test_file, "Early Bird1", 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);
Assert.IsTrue(H5D.get_chunk_info(dset, fspace, index, offset, ref filter_mask, ref addr, ref size) >= 0);
Assert.IsTrue(offset[0] > 0);
Assert.IsTrue(filter_mask == 0 && size > 0 && addr > 0);
Assert.IsTrue(H5D.close(dset) >= 0);
}
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 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);
}
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);
}
static void test_attr_plist()
{
try
{
Console.Write("Testing attribute property lists");
hssize_t[] dims = { 256, 512 };
const string PLST_FILE_NAME = ("tattr_plist.h5");
hssize_t[] dims1 = { SPACE1_DIM1, SPACE1_DIM2, SPACE1_DIM3 };
hssize_t[] dims2 = { ATTR1_DIM };
// Create file.
H5FileId fileId = H5F.create(PLST_FILE_NAME, H5F.CreateMode.ACC_TRUNC);
// Create dataspace for dataset.
H5DataSpaceId space1_Id = H5S.create_simple(SPACE1_RANK, dims1);
// Create a dataset.
H5DataSetId dsetId = H5D.create(fileId, DSET1_NAME, H5T.H5Type.NATIVE_UCHAR, space1_Id);
// Create dataspace for attribute.
H5DataSpaceId space2_Id = H5S.create_simple(ATTR1_RANK, dims2);
// Create default property list for attribute.
H5PropertyListId plist
= H5P.create(H5P.PropertyListClass.ATTRIBUTE_CREATE);
// Create an attribute for the dataset using the property list.
H5AttributeId attrId = H5A.create(dsetId, ATTR1_NAME, new H5DataTypeId(H5T.H5Type.NATIVE_INT), space2_Id, plist);
// Close all objects.
H5S.close(space1_Id);
H5S.close(space2_Id);
H5P.close(plist);
H5A.close(attrId);
H5D.close(dsetId);
H5F.close(fileId);
Console.WriteLine("\t\t\tPASSED");
}
catch (HDFException anyHDF5E)
{
Console.WriteLine(anyHDF5E.Message);
nerrors++;
}
catch (System.Exception sysE)
{
Console.WriteLine(sysE.TargetSite);
Console.WriteLine(sysE.Message);
nerrors++;
}
} // test_attr_plist
/// <summary>
/// Create mapping index - assumes that matrices are square and uses first dimension as the map size
/// </summary>
/// <typeparam name="T"></typeparam>
/// <param name="tazEquiv">array the size of the matrix table dimension</param>
/// <param name="mapDataType">Data type of array</param>
/// <param name="mapName">Name of index map</param>
public void CreateMapping <T>(T[] tazEquiv, H5DataTypeId mapDataType, string mapName)
{
long[] oneDShape = { Shape[0] };
H5DataSpaceId mapSpaceId = H5S.create_simple(1, oneDShape);
H5DataSetId newMappingID = H5D.create(luGroup, mapName, mapDataType, mapSpaceId);
H5D.write(newMappingID, mapDataType, new H5Array <T>(tazEquiv));
IndexMapNames.Add(mapName);
NumIndexMap++;
this.indexMaps.Add(mapName, newMappingID);
}
public void Writer(List <PbTickView> list, string dataset_name)
{
var t = typeof(PbTickStruct5);
var size = Marshal.SizeOf(t);
var typeId = create_type();
// chunk一定得小于dim数据量，多了会出错
// 如果数据100条左右，按
var log10 = (int)Math.Log10(list.Count);
ulong pow = (ulong)Math.Pow(10, log10);
ulong c_s = Math.Min(1000, pow);
ulong[] chunk_size = new ulong[] { c_s };
ulong[] dims = new ulong[] { (ulong)list.Count };
long dcpl = 0;
if (list.Count == 0 || log10 == 0)
{
}
else
{
dcpl = create_property(chunk_size);
}
var spaceid = H5S.create_simple(dims.Length, dims, null);
var datasetid = H5D.create(h5, dataset_name, typeId, spaceid, H5P.DEFAULT, dcpl);
IntPtr p = Marshal.AllocHGlobal(size * (int)dims[0]);
int i = 0;
foreach (var b in list)
{
var s = DataConvert.toStruct(b);
Marshal.StructureToPtr(s, new IntPtr(p.ToInt32() + size * i), false);
++i;
}
H5D.write(datasetid, typeId, spaceid, H5S.ALL, H5P.DEFAULT, p);
H5D.close(datasetid);
H5S.close(spaceid);
H5T.close(typeId);
H5P.close(dcpl);
Marshal.FreeHGlobal(p);
}
public static unsafe void Add(ContainerType container, long fileId, string groupName, string elementName, long typeId, void *dataPtr, long spaceId, long cpl = 0, long apl = 0)
{
long res;
long groupId;
if (H5L.exists(fileId, groupName) > 0)
{
groupId = H5G.open(fileId, groupName);
}
else
{
groupId = H5G.create(fileId, groupName);
}
long id;
if (container == ContainerType.Dataset)
{
id = H5D.create(groupId, Encoding.UTF8.GetBytes(elementName), typeId, spaceId, dcpl_id: cpl, dapl_id: apl);
if (id == -1)
{
throw new Exception("Could not create dataset.");
}
if ((int)dataPtr != 0)
{
res = H5D.write(id, typeId, spaceId, H5S.ALL, 0, new IntPtr(dataPtr));
}
res = H5D.close(id);
}
else
{
id = H5A.create(groupId, Encoding.UTF8.GetBytes(elementName), typeId, spaceId, acpl_id: cpl);
if (id == -1)
{
throw new Exception("Could not create attribute.");
}
if ((int)dataPtr != 0)
{
res = H5A.write(id, typeId, new IntPtr(dataPtr));
}
res = H5A.close(id);
}
res = H5G.close(groupId);
}
private void Write(H5GroupId parent, string name, IMeasurement m)
{
H5DataSpaceId spaceId = H5S.create_simple(1, new long[1] {
(long)1
});
H5DataSetId dataSetId = H5D.create(parent, name, measurement_t, spaceId);
MeasurementT mt = Convert(m);
H5D.writeScalar <MeasurementT>(dataSetId, measurement_t, ref mt);
H5D.close(dataSetId);
H5S.close(spaceId);
}
private void Write(H5GroupId parent, string name, double d)
{
H5DataSpaceId spaceId = H5S.create_simple(1, new long[1] {
1
});
H5DataSetId dataSetId = H5D.create(parent, name, H5T.H5Type.NATIVE_DOUBLE, spaceId);
double data = d;
H5D.writeScalar <double>(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_DOUBLE), ref data);
H5D.close(dataSetId);
H5S.close(spaceId);
}
