public static H5O.info_t GroupInfo(long groupId)
{
H5O.info_t info = new H5O.info_t();
var gid = H5O.get_info(groupId, ref info);
return(info);
}
public void H5Oget_info_by_idxTest2()
{
H5O.info_t info = new H5O.info_t();
Assert.IsFalse(
H5O.get_info_by_idx(Utilities.RandomInvalidHandle(), "A",
H5.index_t.NAME, H5.iter_order_t.NATIVE, 44, ref info) >= 0);
}
public static double ReadAttribute(string file, string dataSetOrGroup, string attribute)
{
double attr = Double.NaN;
try
{
H5FileId fileId = H5F.open(file, H5F.OpenMode.ACC_RDONLY);
H5ObjectInfo objectInfo = H5O.getInfoByName(fileId, dataSetOrGroup);
H5GroupId groupId = null;
H5DataSetId dataSetId = null;
H5AttributeId attrId;
if (objectInfo.objectType == H5ObjectType.GROUP)
{
groupId = H5G.open(fileId, dataSetOrGroup);
attrId = H5A.open(groupId, attribute);
}
else
{
dataSetId = H5D.open(fileId, dataSetOrGroup);
attrId = H5A.open(dataSetId, attribute);
}
H5DataTypeId attrTypeId = H5A.getType(attrId);
double[] dAttrs = new double[] { };
if (H5T.equal(attrTypeId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
{
float[] fAttrs = new float[H5S.getSimpleExtentNPoints(H5A.getSpace(attrId))];
H5A.read(attrId, attrTypeId, new H5Array <float>(fAttrs));
dAttrs = (from f in fAttrs select(double) f).ToArray();
}
else if (H5T.equal(attrTypeId, H5T.copy(H5T.H5Type.NATIVE_DOUBLE)))
{
dAttrs = new double[H5S.getSimpleExtentNPoints(H5A.getSpace(attrId))];
H5A.read(attrId, attrTypeId, new H5Array <double>(dAttrs));
}
H5T.close(attrTypeId);
H5A.close(attrId);
if (groupId != null)
{
H5G.close(groupId);
}
if (dataSetId != null)
{
H5D.close(dataSetId);
}
H5F.close(fileId);
return((double)dAttrs[0]);
}
catch (HDFException e)
{
Console.WriteLine("Error: Unhandled HDF5 exception");
Console.WriteLine(e.Message);
}
return(attr);
}
public static object GetObject(Hdf5Identifier _fileId, AbstractHdf5Object _parent, string _objectName)
{
Hdf5Path combinedPath = _parent.Path.Append(_objectName);
object output = null;
if (combinedPath != null)
{
string fullPath = combinedPath.FullPath;
H5O.info_t gInfo = new H5O.info_t();
H5O.get_info_by_name(_fileId.Value, fullPath, ref gInfo);
var id = H5O.open(_fileId.Value, fullPath).ToId();
if (id.Value > 0)
{
if (gInfo.type == H5O.type_t.DATASET)
{
output = DatasetHelper.LoadDataset(_fileId, id, fullPath);
}
if (gInfo.type == H5O.type_t.GROUP)
{
Hdf5Group group = new Hdf5Group(_fileId, id, fullPath);
group.FileId = _fileId;
group.LoadChildObjects();
output = group;
}
H5O.close(id.Value);
}
}
return(output);
}
private string[] CollectObjects(H5O.type_t type)
{
const int CONTINUE = 0;
int status;
List <string> rv = new List <string>();
// the callback function, called for each item in the iteration
#if HDF5_VER1_10
H5L.iterate_t op_fun = (long loc, IntPtr name, ref H5L.info_t info, IntPtr op_data) =>
#else
H5L.iterate_t op_fun = (int loc, IntPtr name, ref H5L.info_t info, IntPtr op_data) =>
#endif
{
H5O.info_t oinfo = new H5O.info_t();
var bname = Marshal.PtrToStringAnsi(name);
if ((status = H5O.get_info_by_name(loc, bname, ref oinfo, H5P.DEFAULT)) < 0)
{
return(status);
}
if (oinfo.type == type)
{
rv.Add(bname);
}
return(CONTINUE);
};
ulong tracking_index = 0;
if ((status = H5L.iterate(ID, H5.index_t.NAME, H5.iter_order_t.NATIVE, ref tracking_index, op_fun, IntPtr.Zero)) < 0)
{
throw new H5LibraryException($"H5Literate() returned {status}");
}
return(rv.ToArray());
}
public void H5Oexists_by_nameTest1()
{
Assert.IsTrue(H5L.create_soft("/oh my",
m_v0_test_file, "AA") >= 0);
hid_t gid = H5G.create(m_v0_test_file, "A/B/C", m_lcpl);
Assert.IsTrue(gid >= 0);
Assert.IsTrue(H5O.exists_by_name(m_v0_test_file, "A/B") > 0);
Assert.IsTrue(H5O.exists_by_name(m_v0_test_file, "AA") == 0);
Assert.IsTrue(
H5O.exists_by_name(m_v0_test_file, "A/B/Caesar") < 0);
Assert.IsTrue(H5G.close(gid) >= 0);
Assert.IsTrue(H5L.create_soft("/oh my",
m_v2_test_file, "AA") >= 0);
gid = H5G.create(m_v2_test_file, "A/B/C", m_lcpl);
Assert.IsTrue(gid >= 0);
Assert.IsTrue(H5O.exists_by_name(m_v2_test_file, "A/B") > 0);
Assert.IsTrue(H5O.exists_by_name(m_v2_test_file, "AA") == 0);
Assert.IsTrue(
H5O.exists_by_name(m_v2_test_file, "A/B/Caesar") < 0);
Assert.IsTrue(H5G.close(gid) >= 0);
}
public static bool GroupExists(hid_t groupId, string groupName)
{
H5O.info_t info = new H5O.info_t();
var gid = H5O.get_info_by_name(groupId, groupName, ref info, H5P.DEFAULT);
return(gid == 0);
}
public void H5OvisitTest1()
{
Assert.IsTrue(H5G.create(m_v0_test_file, "A/B/C/D", m_lcpl) >= 0);
Assert.IsTrue(
H5L.create_hard(m_v0_test_file, "A/B/C/D", m_v0_test_file,
"shortcut") >= 0);
Assert.IsTrue(H5G.create(m_v2_test_file, "A/B/C/D", m_lcpl) >= 0);
Assert.IsTrue(
H5L.create_hard(m_v2_test_file, "A/B/C/D", m_v2_test_file,
"shortcut") >= 0);
ArrayList al = new ArrayList();
GCHandle hnd = GCHandle.Alloc(al);
IntPtr op_data = (IntPtr)hnd;
// the callback is defined in H5LTest.cs
H5O.iterate_t cb = DelegateMethod;
Assert.IsTrue(H5O.visit(m_v0_test_file, H5.index_t.NAME,
H5.iter_order_t.NATIVE, cb, op_data) >= 0);
// we should have 5 elements in the array list
Assert.IsTrue(al.Count == 5);
Assert.IsTrue(H5O.visit(m_v2_test_file, H5.index_t.NAME,
H5.iter_order_t.NATIVE, cb, op_data) >= 0);
// we should have 10 (5 + 5) elements in the array list
Assert.IsTrue(al.Count == 10);
hnd.Free();
}
public void H5OvisitTest2()
{
string path = String.Join("/", m_utf8strings);
Assert.IsTrue(H5G.create(m_v0_test_file,
Encoding.UTF8.GetBytes(path), m_lcpl_utf8) >= 0);
Assert.IsTrue(H5G.create(m_v2_test_file,
Encoding.UTF8.GetBytes(path), m_lcpl_utf8) >= 0);
ArrayList al = new ArrayList();
GCHandle hnd = GCHandle.Alloc(al);
IntPtr op_data = (IntPtr)hnd;
// the callback is defined in H5LTest.cs
H5O.iterate_t cb = DelegateMethod;
Assert.IsTrue(H5O.visit(m_v0_test_file, H5.index_t.NAME,
H5.iter_order_t.NATIVE, cb, op_data) >= 0);
// we should have 6 elements in the array list
Assert.IsTrue(al.Count == 6);
Assert.IsTrue(H5O.visit(m_v2_test_file, H5.index_t.NAME,
H5.iter_order_t.NATIVE, cb, op_data) >= 0);
// we should have 12 (6 + 6) elements in the array list
Assert.IsTrue(al.Count == 12);
hnd.Free();
}
public void H5Oget_info_by_nameTest2()
{
H5O.info_t info = new H5O.info_t();
Assert.IsFalse(
H5O.get_info_by_name(Utilities.RandomInvalidHandle(), ".",
ref info) >= 0);
}
public void H5Oget_info_by_idxTest1()
{
Assert.IsTrue(
H5G.close(H5G.create(m_v0_test_file, "A")) >= 0);
Assert.IsTrue(
H5G.close(H5G.create(m_v0_test_file, "AA")) >= 0);
Assert.IsTrue(
H5G.close(H5G.create(m_v0_test_file, "AAA")) >= 0);
Assert.IsTrue(
H5G.close(H5G.create(m_v0_test_file, "AAAA")) >= 0);
H5O.info_t info = new H5O.info_t();
Assert.IsTrue(H5O.get_info_by_idx(m_v0_test_file, ".",
H5.index_t.NAME, H5.iter_order_t.NATIVE, 2, ref info) >= 0);
Assert.IsTrue(info.type == H5O.type_t.GROUP);
Assert.IsTrue(
H5G.close(H5G.create(m_v2_test_file, "A")) >= 0);
Assert.IsTrue(
H5G.close(H5G.create(m_v2_test_file, "AA")) >= 0);
Assert.IsTrue(
H5G.close(H5G.create(m_v2_test_file, "AAA")) >= 0);
Assert.IsTrue(
H5G.close(H5G.create(m_v2_test_file, "AAAA")) >= 0);
info = new H5O.info_t();
Assert.IsTrue(H5O.get_info_by_idx(m_v2_test_file, ".",
H5.index_t.NAME, H5.iter_order_t.NATIVE, 2, ref info) >= 0);
Assert.IsTrue(info.type == H5O.type_t.GROUP);
}
protected Dictionary <string, long> FindChildren(bool dataSets)
{
Dictionary <string, long> datasetNames = new Dictionary <string, long>();
Dictionary <string, long> groupNames = new Dictionary <string, long>();
var rootID = Open();
ulong dummy = 0;
H5L.iterate(rootID, H5.index_t.NAME, H5.iter_order_t.INC, ref dummy, new H5L.iterate_t(
delegate(long objectId, IntPtr namePtr, ref H5L.info_t info, IntPtr op_data)
{
string objectName = Marshal.PtrToStringAnsi(namePtr);
H5O.info_t gInfo = new H5O.info_t();
H5O.get_info_by_name(objectId, objectName, ref gInfo);
if (gInfo.type == H5O.type_t.DATASET)
{
datasetNames[objectName] = objectId;
}
else if (gInfo.type == H5O.type_t.GROUP)
{
groupNames[objectName] = objectId;
}
return(0);
}), new IntPtr());
H5G.close(rootID);
if (dataSets)
{
return(datasetNames);
}
return(groupNames);
}
/// <summary>
/// Add an attribute and write the values to the file
/// </summary>
/// <typeparam name="T"></typeparam>
/// <param name="_name"></param>
/// <param name="_value"></param>
/// <returns></returns>
public Hdf5Attribute Add <T>(string _name, T _value)
{
if (Exists(_name))
{
throw new Hdf5AttributeAlreadyExistException();
}
//If the parent is the file, then just create the attribute (file already open).
if (ParentObject.Id.Equals(ParentObject.FileId))
{
return(AttributeHelper.CreateAttributeAddToList(ParentObject.Id, this, _name, _value));
}
Hdf5Attribute attribute = null;
//Otherwise open the object and then call the function.
var id = H5O.open(ParentObject.FileId.Value, ParentObject.Path.FullPath).ToId();
if (id.Value > 0)
{
attribute = AttributeHelper.CreateAttributeAddToList(id, this, _name, _value);
H5O.close(id.Value);
}
return(attribute);
}
// Function used with H5L.iterate
protected H5IterationResult Op_Func(H5GroupId id,
string objectName,
H5LinkInfo info, Object param)
{
H5ObjectInfo objInfo = H5O.getInfoByName(id, objectName);
string groupName = (string)param;
switch (objInfo.objectType)
{
case H5ObjectType.DATASET:
OnHdfObjInfoFound(objectName, HdfObjectType.Dataset, groupName);
break;
case H5ObjectType.GROUP:
GetHdfObjInfo(objectName);
break;
case H5ObjectType.NAMED_DATATYPE:
break;
case H5ObjectType.UNKNOWN:
break;
}
return(H5IterationResult.SUCCESS);
}
public static bool GroupExists(hid_t hid, string groupName)
{
if (string.IsNullOrEmpty(groupName))
{
throw new ArgumentException("groupName");
}
var exists = H5L.exists(hid, groupName);
if (exists < 0)
{
throw new HDF5Exception("H5L.exists failed");
}
if (exists == 0)
{
return(false);
}
var objectId = H5O.open(hid, groupName);
if (objectId < 0)
{
throw new HDF5Exception("H5O.open failed");
}
var result = GroupExists(objectId);
H5O.close(objectId);
return(result);
}
public static void Write1DArray <T>(Hdf5Dataset _dataset, T[] _array)
{
if (_dataset.Dataspace.NumberOfDimensions != 1)
{
throw new Hdf5ArrayDimensionsMismatchException();
}
if ((ulong)_array.Length != _dataset.Dataspace.DimensionProperties[0].CurrentSize)
{
throw new Hdf5ArraySizeMismatchException();
}
var datasetId = H5O.open(_dataset.FileId.Value, _dataset.Path.FullPath).ToId();
GCHandle arrayHandle = GCHandle.Alloc(_array, GCHandleType.Pinned);
var typeId = H5T.copy(_dataset.DataType.NativeType.Value).ToId();
int result = H5D.write(
datasetId.Value,
typeId.Value,
H5S.ALL,
H5S.ALL,
H5P.DEFAULT,
arrayHandle.AddrOfPinnedObject());
arrayHandle.Free();
H5T.close(typeId.Value);
H5O.close(datasetId.Value);
FileHelper.FlushToFile(_dataset.FileId);
}
public static ulong NumberOfAttributes(int groupId, string groupName)
{
H5O.info_t info = new H5O.info_t();
var gid = H5O.get_info(groupId, ref info);
return(info.num_attrs);
}
public void H5OcopyTest2()
{
Assert.IsTrue(H5L.create_soft("/my/fantastic/path",
m_v0_test_file, "A") >= 0);
Assert.IsTrue(H5O.copy(m_v0_test_file, ".", m_v2_test_file,
"C/B/A_copy", H5P.DEFAULT, m_lcpl) >= 0);
}
public void H5OcloseTest4()
{
hid_t space = H5S.create(H5S.class_t.SCALAR);
Assert.IsTrue(space >= 0);
Assert.IsTrue(H5O.close(space) < 0);
Assert.IsTrue(H5S.close(space) >= 0);
}
public void H5Odisable_mdc_flushesTestSWMR2()
{
hid_t grp = H5G.create(m_v3_test_file_no_swmr, "/A/B/C", m_lcpl);
Assert.IsTrue(grp >= 0);
Assert.IsTrue(H5O.disable_mdc_flushes(grp) >= 0);
Assert.IsTrue(H5G.flush(grp) >= 0);
Assert.IsTrue(H5G.close(grp) >= 0);
}
public void H5OcloseTest1()
{
hid_t gid = H5G.create(m_v0_test_file, "A");
Assert.IsTrue(gid >= 0);
Assert.IsTrue(H5O.close(gid) >= 0);
gid = H5G.create(m_v2_test_file, "A");
Assert.IsTrue(gid >= 0);
Assert.IsTrue(H5O.close(gid) >= 0);
}
public void H5Oopen_by_idxTest2()
{
Assert.IsFalse(
H5O.open_by_idx(Utilities.RandomInvalidHandle(), ".",
H5.index_t.NAME, H5.iter_order_t.NATIVE,
44) >= 0);
Assert.IsFalse(
H5O.open_by_idx(m_v2_class_file, ".",
H5.index_t.NAME, H5.iter_order_t.NATIVE,
hsize_t.MaxValue) >= 0);
}
public static Dictionary <H5I.type_t, List <string> > IterateObject2(hid_t hid)
{
var objects = new Dictionary <H5I.type_t, List <string> >();
H5O.visit(hid, H5.index_t.NAME, H5.iter_order_t.INC,
new H5O.iterate_t(
delegate(hid_t objectId, IntPtr namePtr, ref H5O.info_t info, IntPtr data)
{
var objectName = Marshal.PtrToStringAnsi(namePtr);
switch (H5I.get_type(objectId))
{
case H5I.type_t.GROUP:
if (!objects.ContainsKey(H5I.type_t.GROUP))
{
objects[H5I.type_t.GROUP] = new List <string>();
}
objects[H5I.type_t.GROUP].Add(objectName);
break;
case H5I.type_t.DATASET:
if (!objects.ContainsKey(H5I.type_t.DATASET))
{
objects[H5I.type_t.DATASET] = new List <string>();
}
objects[H5I.type_t.DATASET].Add(objectName);
break;
case H5I.type_t.DATATYPE:
if (!objects.ContainsKey(H5I.type_t.DATATYPE))
{
objects[H5I.type_t.DATATYPE] = new List <string>();
}
objects[H5I.type_t.DATATYPE].Add(objectName);
break;
case H5I.type_t.ATTR:
if (!objects.ContainsKey(H5I.type_t.ATTR))
{
objects[H5I.type_t.ATTR] = new List <string>();
}
objects[H5I.type_t.ATTR].Add(objectName);
break;
default:
break;
}
return(0);
}), IntPtr.Zero);
return(objects);
}
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 H5OcopyTest1()
{
hid_t gid = H5G.create(m_v0_test_file, "A/B/C", m_lcpl);
Assert.IsTrue(gid >= 0);
Assert.IsTrue(
H5O.copy(m_v0_test_file, "A", m_v2_test_file, "A_copy") >= 0);
Assert.IsTrue(H5L.exists(m_v2_test_file, "A_copy/B/C") > 0);
Assert.IsTrue(H5G.close(gid) >= 0);
}
public void H5OopenTest1()
{
Assert.IsTrue(
H5G.close(H5G.create(m_v0_test_file, "A/B/C", m_lcpl)) >= 0);
hid_t obj = H5O.open(m_v0_test_file, "A/B");
Assert.IsTrue(obj >= 0);
Assert.IsTrue(H5O.close(obj) >= 0);
Assert.IsTrue(
H5G.close(H5G.create(m_v2_test_file, "A/B/C", m_lcpl)) >= 0);
obj = H5O.open(m_v2_test_file, "A/B");
Assert.IsTrue(obj >= 0);
Assert.IsTrue(H5O.close(obj) >= 0);
}
public void H5OlinkTest1()
{
hid_t gid = H5G.create_anon(m_v0_test_file);
Assert.IsTrue(gid >= 0);
Assert.IsTrue(H5O.link(gid, m_v0_test_file, "A/B/C", m_lcpl) >= 0);
Assert.IsTrue(H5G.close(gid) >= 0);
gid = H5G.create_anon(m_v2_test_file);
Assert.IsTrue(gid >= 0);
Assert.IsTrue(H5O.link(gid, m_v2_test_file, "A/B/C", m_lcpl) >= 0);
Assert.IsTrue(H5G.close(gid) >= 0);
}
/// <summary>
/// Update the attribute and write the values to the file
/// </summary>
/// <param name="_attribute"></param>
public void Update(Hdf5Attribute _attribute)
{
//If the parent is the file, then just update the attribute (file already open).
if (ParentObject.Id.Equals(ParentObject.FileId))
{
AttributeHelper.UpdateAttribute(ParentObject.Id, _attribute);
}
//Otherwise open the object and then update the attribute.
var id = H5O.open(ParentObject.FileId.Value, ParentObject.Path.FullPath).ToId();
if (id.Value > 0)
{
AttributeHelper.UpdateAttribute(id, _attribute);
H5O.close(id.Value);
}
}
public void H5Oget_info_by_nameTest1()
{
Assert.IsTrue(
H5G.close(H5G.create(m_v0_test_file, "A/B/C", m_lcpl)) >= 0);
H5O.info_t info = new H5O.info_t();
Assert.IsTrue(
H5O.get_info_by_name(m_v0_test_file, "A/B", ref info) >= 0);
Assert.IsTrue(info.type == H5O.type_t.GROUP);
Assert.IsTrue(
H5G.close(H5G.create(m_v2_test_file, "A/B/C", m_lcpl)) >= 0);
info = new H5O.info_t();
Assert.IsTrue(
H5O.get_info_by_name(m_v2_test_file, "A/B", ref info) >= 0);
Assert.IsTrue(info.type == H5O.type_t.GROUP);
}
public void H5Odecr_refcountTest1()
{
hid_t gid = H5G.create(m_v0_test_file, "A/B/C", m_lcpl);
Assert.IsTrue(gid >= 0);
// Don't try this at home!
Assert.IsTrue(H5O.decr_refcount(gid) >= 0);
Assert.IsTrue(H5G.close(gid) >= 0);
gid = H5G.create(m_v2_test_file, "A/B/C", m_lcpl);
Assert.IsTrue(gid >= 0);
// Don't try this at home!
Assert.IsTrue(H5O.decr_refcount(gid) >= 0);
Assert.IsTrue(H5G.close(gid) >= 0);
}
