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 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);
}
// Matrix Specific Methods
// TODO:
// 1. add handling for matrix title
// 2. add specification of NA values
// 3. other attributes: pa-format flag, year int, source string
/// <summary>
/// Returns a row of the matrix
/// </summary>
/// <typeparam name="T"></typeparam>
/// <param name="matName"></param>
/// <param name="rowIndex"></param>
/// <returns></returns>
public T[] GetMatrixRow <T>(string matName, int rowIndex)
{
var rowData = new T[Shape[1]];
// check that matrix exists
if (tables.ContainsKey(matName))
{
H5DataSetId matId;
tables.TryGetValue(matName, out matId);
H5DataTypeId matDataId = H5D.getType(matId);
H5DataSpaceId spaceId = H5S.create_simple(2, Shape);
var h5matrix = new H5Array <T>(rowData);
long[] start = { rowIndex, 0 };
long[] count = { 1, Shape[1] };
H5S.selectHyperslab(spaceId, H5S.SelectOperator.SET, start, count);
H5DataSpaceId readSpaceId = H5S.create_simple(2, count);
H5D.read(matId, matDataId, readSpaceId, spaceId, H5P.create(H5P.PropertyListClass.DATASET_XFER), h5matrix);
H5S.close(spaceId);
H5S.close(readSpaceId);
}
else
{
Console.WriteLine("table {0} not found in matrix file", matName);
}
return(rowData);
}
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);
}
public void H5Pset_mdc_image_configTest1()
{
hid_t fapl = H5P.create(H5P.FILE_ACCESS);
Assert.IsTrue(fapl >= 0);
Assert.IsTrue(H5P.set_libver_bounds(fapl, H5F.libver_t.LATEST) >= 0);
H5AC.cache_image_config_t conf = new H5AC.cache_image_config_t();
conf.version = H5AC.CURR_CACHE_IMAGE_CONFIG_VERSION;
conf.entry_ageout = H5AC.CACHE_IMAGE__ENTRY_AGEOUT__NONE;
IntPtr config_ptr = Marshal.AllocHGlobal(Marshal.SizeOf(conf));
Marshal.StructureToPtr(conf, config_ptr, false);
H5AC.cache_image_config_t conf1 = new H5AC.cache_image_config_t();
conf1 = (H5AC.cache_image_config_t)Marshal.PtrToStructure(
config_ptr, typeof(H5AC.cache_image_config_t));
//Assert.IsTrue(H5P.set_mdc_image_config(fapl, config_ptr) >= 0);
Assert.IsTrue(H5P.close(fapl) >= 0);
Marshal.FreeHGlobal(config_ptr);
}
/// <summary>
/// Create a temporary HDF5 with SWMR access and return
/// its name and a file handle.
/// </summary>
public static hid_t H5TempFileSWMR(ref string fileName)
{
hid_t fapl = H5P.create(H5P.FILE_ACCESS);
if (fapl < 0)
{
throw new ApplicationException("H5P.create failed.");
}
if (H5P.set_libver_bounds(fapl, H5F.libver_t.LATEST) < 0)
{
throw new ApplicationException("H5P.set_libver_bounds failed.");
}
if (H5P.set_fclose_degree(fapl, H5F.close_degree_t.STRONG) < 0)
{
throw new ApplicationException("H5P.set_fclose_degree failed.");
}
fileName = Path.GetTempFileName();
hid_t file = H5F.create(fileName, H5F.ACC_TRUNC | H5F.ACC_SWMR_WRITE,
H5P.DEFAULT, fapl);
if (file < 0)
{
throw new ApplicationException("H5F.create failed.");
}
if (H5P.close(fapl) < 0)
{
throw new ApplicationException("H5P.close failed.");
}
return(file);
}
public void H5Dcreate_anonTest2()
{
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 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_anon(m_v0_test_file, H5T.IEEE_F32BE,
space, dcpl);
Assert.IsTrue(dset >= 0);
Assert.IsTrue(H5D.close(dset) >= 0);
dset = H5D.create_anon(m_v2_test_file, H5T.IEEE_F32BE,
space, dcpl);
Assert.IsTrue(dset >= 0);
Assert.IsTrue(H5D.close(dset) >= 0);
Assert.IsTrue(H5P.close(dcpl) >= 0);
Assert.IsTrue(H5S.close(space) >= 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 H5Pset_append_flushTestSWMR2()
{
hid_t dapl = H5P.create(H5P.DATASET_ACCESS);
Assert.IsTrue(dapl >= 0);
hsize_t[] boundary = { 1, 1 };
H5D.append_cb_t cb = append_func;
Assert.IsTrue(
H5P.set_append_flush(dapl, 2, boundary, cb, IntPtr.Zero) >= 0);
hsize_t[] check_boundary = { 0, 0, 0 };
H5D.append_cb_t check_cb = null;
IntPtr check_ptr = new IntPtr(4711);
Assert.IsTrue(
H5P.get_append_flush(dapl, 2, check_boundary, ref check_cb,
ref check_ptr) >= 0);
Assert.IsTrue(check_boundary[0] == 1);
Assert.IsTrue(check_boundary[1] == 1);
Assert.IsTrue(check_boundary[2] == 0);
Assert.IsTrue(check_cb == cb);
Assert.IsTrue(check_ptr == IntPtr.Zero);
Assert.IsTrue(H5P.close(dapl) >= 0);
}
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 static unsafe void AddMass(long fileId, ContainerType container)
{
long res;
var typeId = TestUtils.GetHdfTypeIdFromType(typeof(TestStructL1));
for (int i = 0; i < 1000; i++)
{
var dims = new ulong[] { 2, 2, 3 };
if (i == 450)
{
var acpl_id = H5P.create(H5P.ATTRIBUTE_CREATE);
res = H5P.set_char_encoding(acpl_id, H5T.cset_t.UTF8);
var name = "字形碼 / 字形码, Zìxíngmǎ";
TestUtils.Add(container, fileId, "mass_attributes", name, typeId, TestData.NonNullableStructData.AsSpan(), dims, cpl: acpl_id);
}
else
{
var name = $"mass_{i.ToString("D4")}";
TestUtils.Add(container, fileId, "mass_attributes", name, typeId, TestData.NonNullableStructData.AsSpan(), dims);
}
}
res = H5T.close(typeId);
}
/// <summary>
/// Writes the entire matrix table
/// </summary>
/// <typeparam name="T"></typeparam>
/// <param name="matName"></param>
/// <param name="rowIndex"></param>
/// <returns></returns>
public void SetMatrix <T>(string matName, T[,] data)
{
// check that matrix exists
if (tables.ContainsKey(matName))
{
H5DataSetId matId;
tables.TryGetValue(matName, out matId);
H5DataTypeId matDataId = H5D.getType(matId);
H5DataSpaceId spaceId = H5S.create_simple(2, Shape);
long[] start = { 0, 0 };
long[] count = { Shape[0], Shape[1] };
var h5matrix = new H5Array <T>(data);
H5S.selectHyperslab(spaceId, H5S.SelectOperator.SET, start, count);
H5DataSpaceId readSpaceId = H5S.create_simple(2, count);
H5D.write(matId, matDataId, readSpaceId, spaceId, H5P.create(H5P.PropertyListClass.DATASET_XFER), h5matrix);
H5S.close(spaceId);
H5S.close(readSpaceId);
}
else
{
Console.WriteLine("table {0} not found in matrix file", matName);
}
return;
}
public void H5Pset_object_flush_cbTestSWMR2()
{
hid_t fapl = H5P.create(H5P.FILE_ACCESS);
Assert.IsTrue(fapl >= 0);
H5F.flush_cb_t cb = flush_func;
Assert.IsTrue(
H5P.set_object_flush_cb(fapl, cb, IntPtr.Zero) >= 0);
H5F.flush_cb_t check_cb = null;
IntPtr check_ptr = new IntPtr(4711);
Assert.IsTrue(
H5P.get_object_flush_cb(fapl, ref check_cb,
ref check_ptr) >= 0);
Assert.IsTrue(check_cb == cb);
Assert.IsTrue(check_ptr == IntPtr.Zero);
Assert.IsTrue(H5P.close(fapl) >= 0);
}
/// <summary>
/// Create a temporary HDF5 file IN MEMORY and return its name and
/// a file handle.
/// </summary>
public static hid_t H5TempFile(ref string fileName,
H5F.libver_t version = H5F.libver_t.LATEST,
bool backing_store = false)
{
hid_t fapl = H5P.create(H5P.FILE_ACCESS);
if (fapl < 0)
{
throw new ApplicationException("H5P.create failed.");
}
if (H5P.set_libver_bounds(fapl, version) < 0)
{
throw new ApplicationException("H5P.set_libver_bounds failed.");
}
// use the core VFD, 64K increments, no backing store
if (H5P.set_fapl_core(fapl, new IntPtr(65536),
(uint)(backing_store ? 1 : 0)) < 0)
{
throw new ApplicationException("H5P.set_fapl_core failed.");
}
fileName = Path.GetTempFileName();
hid_t file = H5F.create(fileName, H5F.ACC_TRUNC, H5P.DEFAULT, fapl);
if (file < 0)
{
throw new ApplicationException("H5F.create failed.");
}
if (H5P.close(fapl) < 0)
{
throw new ApplicationException("H5P.close failed.");
}
return(file);
}
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 unsafe void AddExternalDataset(long fileId, string datasetName, string absolutePrefix, H5DatasetAccess datasetAccess)
{
long res;
var bytesoftype = 4;
var dcpl_id = H5P.create(H5P.DATASET_CREATE);
var dapl_id = H5P.create(H5P.DATASET_ACCESS);
res = H5P.set_layout(dcpl_id, H5D.layout_t.CONTIGUOUS);
// a (more than one chunk in file)
var pathA = H5Utils.ConstructExternalFilePath(Path.Combine(absolutePrefix, $"{datasetName}_a.raw"), datasetAccess);
if (File.Exists(pathA))
{
File.Delete(pathA);
}
res = H5P.set_external(dcpl_id, pathA, new IntPtr(120), (ulong)(10 * bytesoftype));
res = H5P.set_external(dcpl_id, pathA, new IntPtr(80), (ulong)(10 * bytesoftype));
res = H5P.set_external(dcpl_id, pathA, new IntPtr(0), (ulong)(10 * bytesoftype));
// b (file size smaller than set size)
var pathB = H5Utils.ConstructExternalFilePath(Path.Combine(absolutePrefix, $"{datasetName}_b.raw"), datasetAccess);
if (File.Exists(pathB))
{
File.Delete(pathB);
}
res = H5P.set_external(dcpl_id, pathB, new IntPtr(0), (ulong)(10 * bytesoftype));
// c (normal file)
var pathC = H5Utils.ConstructExternalFilePath(Path.Combine(absolutePrefix, $"{datasetName}_c.raw"), datasetAccess);
if (File.Exists(pathC))
{
File.Delete(pathC);
}
res = H5P.set_external(dcpl_id, pathC, new IntPtr(0), (ulong)((TestData.MediumData.Length - 40) * bytesoftype));
// write data
if (datasetAccess.ExternalFilePrefix is not null)
{
H5P.set_efile_prefix(dapl_id, datasetAccess.ExternalFilePrefix);
}
TestUtils.Add(ContainerType.Dataset, fileId, "external", datasetName, H5T.NATIVE_INT32, TestData.MediumData.AsSpan(), apl: dapl_id, cpl: dcpl_id);
// truncate file b
using (var fileStream2 = File.OpenWrite(pathB))
{
fileStream2.SetLength(10);
};
res = H5P.close(dapl_id);
res = H5P.close(dcpl_id);
}
public void H5Pset_evict_on_closeTest2()
{
hid_t fcpl = H5P.create(H5P.FILE_CREATE);
Assert.IsTrue(fcpl >= 0);
Assert.IsFalse(H5P.set_evict_on_close(fcpl, 1) >= 0);
Assert.IsTrue(H5P.close(fcpl) >= 0);
}
public void H5Pset_evict_on_closeTest1()
{
hid_t fapl = H5P.create(H5P.FILE_ACCESS);
Assert.IsTrue(fapl >= 0);
Assert.IsTrue(H5P.set_evict_on_close(fapl, 1) >= 0);
Assert.IsTrue(H5P.close(fapl) >= 0);
}
public void H5Pset_userblockTest1()
{
hid_t fcpl = H5P.create(H5P.FILE_CREATE);
Assert.IsTrue(fcpl >= 0);
Assert.IsTrue(H5P.set_userblock(fcpl, 1024) >= 0);
Assert.IsTrue(H5P.close(fcpl) >= 0);
}
private static long create_property(ulong[] chunk_size)
{
var dcpl = H5P.create(H5P.DATASET_CREATE);
H5P.set_layout(dcpl, H5D.layout_t.CHUNKED);
H5P.set_chunk(dcpl, chunk_size.Length, chunk_size);
H5P.set_deflate(dcpl, 6);
return(dcpl);
}
private void Menu_2()
{
long vdsFileId = -1;
long vdsMetaFileId = -1;
long fcPropertyId = -1;
string vdsFilePath;
string vdsMetaFilePath;
List <CampaignInfo> campaignInfoSet;
IList <HdfElementBase> currentList;
//
vdsFilePath = Path.Combine(Program.BaseDirectoryPath, "VDS.h5");
vdsMetaFilePath = Path.Combine(Program.BaseDirectoryPath, "VDS_META.h5");
try
{
if (File.Exists(vdsFilePath))
{
vdsFileId = H5F.open(vdsFilePath, H5F.ACC_RDONLY);
}
else
{
return;
}
if (File.Exists(vdsMetaFilePath))
{
vdsMetaFileId = H5F.open(vdsMetaFilePath, H5F.ACC_RDWR);
}
if (vdsMetaFileId == -1)
{
fcPropertyId = H5P.create(H5P.FILE_CREATE);
H5P.set_file_space(fcPropertyId, H5F.file_space_type_t.ALL_PERSIST);
vdsMetaFileId = H5F.create(vdsMetaFilePath, H5F.ACC_TRUNC, fcPropertyId);
}
campaignInfoSet = GeneralHelper.GetCampaignInfoSet(vdsFileId, true);
currentList = campaignInfoSet.Cast <HdfElementBase>().ToList();
new VdsMetaNavigator(vdsFileId, vdsMetaFileId, "/", currentList);
}
finally
{
if (H5I.is_valid(vdsFileId) > 0)
{
H5F.close(vdsFileId);
}
if (H5I.is_valid(vdsMetaFileId) > 0)
{
H5F.close(vdsMetaFileId);
}
}
}
public static unsafe void AddCompactDataset(long fileId)
{
long res;
var dcpl_id = H5P.create(H5P.DATASET_CREATE);
res = H5P.set_layout(dcpl_id, H5D.layout_t.COMPACT);
TestUtils.Add(ContainerType.Dataset, fileId, "compact", "compact", H5T.NATIVE_INT32, TestData.SmallData.AsSpan(), cpl: dcpl_id);
res = H5P.close(dcpl_id);
}
public void H5Pset_userblockTest3()
{
hid_t fcpl = H5P.create(H5P.FILE_CREATE);
Assert.IsTrue(fcpl >= 0);
Assert.IsTrue(H5P.set_userblock(fcpl, 0) >= 0);
Assert.IsFalse(H5P.set_userblock(fcpl, 111) >= 0);
Assert.IsTrue(H5P.set_userblock(fcpl, 512) >= 0);
Assert.IsFalse(H5P.set_userblock(fcpl, 513) >= 0);
Assert.IsTrue(H5P.close(fcpl) >= 0);
}
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 static void ClassInit(TestContext testContext)
{
hid_t fapl = H5P.create(H5P.FILE_ACCESS);
Assert.IsTrue(fapl >= 0);
Assert.IsTrue(
H5P.set_libver_bounds(fapl, H5F.libver_t.LATEST) >= 0);
m_shared_file_id = H5F.create(m_shared_file_name, H5F.ACC_TRUNC,
H5P.DEFAULT, fapl);
Assert.IsTrue(H5P.close(fapl) >= 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
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);
}