public Dictionary <string, string> TryReadDataTable(string datasetName)
{
Dictionary <string, string> result = null;
var subDsDic = ds.GetSubDatasets();
if (subDsDic.Count > 0)
{
H5ID h5FileId = H5F.open(fileName, H5F.ACC_RDONLY);
H5ID datasetId = H5D.open(h5FileId, datasetName);
H5ID typeId = H5D.get_type(datasetId);
H5ID spaceId = H5D.get_space(datasetId);
if (H5T.get_class(typeId) == H5T.class_t.COMPOUND)
{
int numCount = H5T.get_nmembers(typeId);
var size = H5T.get_size(typeId);
byte[] buffer = new byte[size.ToInt32()];
GCHandle hnd = GCHandle.Alloc(buffer, GCHandleType.Pinned);
int ndims = H5S.get_simple_extent_ndims(spaceId);
if (ndims == 1)
{
result = new Dictionary <string, string>();
H5D.read(datasetId, typeId, H5S.ALL, H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject());
for (uint i = 0; i < numCount; i++)
{
string name = Marshal.PtrToStringAnsi(H5T.get_member_name(typeId, i));
int offset = H5T.get_member_offset(typeId, i).ToInt32();
H5ID subTypeId = H5T.get_member_type(typeId, i);
H5T.class_t typeClass = H5T.get_member_class(typeId, i);
string value = ReadBuffer(buffer, offset, typeClass, subTypeId);
result.Add(name, value);
H5T.close(subTypeId);
}
}
hnd.Free();
}
if (spaceId != 0)
{
H5S.close(spaceId);
}
if (typeId != 0)
{
H5T.close(typeId);
}
if (datasetId != 0)
{
H5D.close(datasetId);
}
if (h5FileId != 0)
{
H5F.close(h5FileId);
}
}
return(result);
}
private static bool IsHDF5String(hid_t fileLoc, string name)
{
hid_t dset = H5D.open(fileLoc, name);
hid_t type = H5D.get_type(dset);
H5T.class_t cl = H5T.get_class(type);
return(cl == H5T.class_t.STRING);
}
private string ReadBuffer(byte[] buffer, int offset, H5T.class_t typeClass, int typeId)
{
string result = string.Empty;
IntPtr dataSize = H5T.get_size(typeId);
H5T.order_t order = H5T.get_order(typeId);
byte[] temp = new byte[dataSize.ToInt32()];
Array.Copy(buffer, offset, temp, 0, dataSize.ToInt32());
if (order == H5T.order_t.BE && typeClass != H5T.class_t.STRING)
{
Array.Reverse(temp);
}
switch (typeClass)
{
case H5T.class_t.NO_CLASS:
break;
case H5T.class_t.INTEGER:
// H5T.Sign.TWOS_COMPLEMENT;
H5T.sign_t sign = H5T.get_sign(typeId);
switch (dataSize.ToInt32())
{
case 1:
result = ((double)BitConverter.ToChar(temp, 0)).ToString("G");
break;
case 2:
switch (sign)
{
case H5T.sign_t.SGN_2:
result = ((double)BitConverter.ToInt16(temp, 0)).ToString("G");
break;
case H5T.sign_t.NONE:
result = ((double)BitConverter.ToUInt16(temp, 0)).ToString("G");
break;
}
break;
case 4:
switch (sign)
{
case H5T.sign_t.SGN_2:
result = ((double)BitConverter.ToInt32(temp, 0)).ToString("G");
break;
case H5T.sign_t.NONE:
result = ((double)BitConverter.ToUInt32(temp, 0)).ToString("G");
break;
}
break;
case 8:
switch (sign)
{
case H5T.sign_t.SGN_2:
result = ((double)BitConverter.ToInt64(temp, 0)).ToString("G");
break;
case H5T.sign_t.NONE:
result = ((double)BitConverter.ToUInt64(temp, 0)).ToString("G");
break;
}
break;
}
break;
case H5T.class_t.FLOAT:
switch (dataSize.ToInt32())
{
case 4:
{
result = BitConverter.ToSingle(temp, 0).ToString("G");
break;
}
case 8:
{
result = BitConverter.ToDouble(temp, 0).ToString("G");
break;
}
}
break;
case H5T.class_t.STRING:
{
GCHandle handler = GCHandle.Alloc(temp, GCHandleType.Pinned);
var str = Marshal.PtrToStringAnsi(handler.AddrOfPinnedObject());
handler.Free();
result = str;
break;
}
default:
break;
}
return(result);
}
public Dictionary <string, string> GetDatasetAttributes(string originalDatasetName)
{
H5DataSetId datasetId = 0;
H5GroupId groupId = 0;
H5DataTypeId typeId = 0;
H5DataSpaceId spaceId = 0;
try
{
if (_h5FileId < 0)
{
return(null);
}
string datasetName = GetDatasetFullNames(originalDatasetName, _h5FileId);
if (string.IsNullOrEmpty(datasetName))
{
return(null);
}
int groupIndex = datasetName.LastIndexOf('/');
if (groupIndex == -1)
{
datasetId = H5D.open(_h5FileId, datasetName);
}
else
{
string groupName = datasetName.Substring(0, groupIndex + 1);
string dsName = datasetName.Substring(groupIndex + 1);
groupId = H5G.open(_h5FileId, groupName);
datasetId = H5D.open(groupId, dsName);
}
if (datasetId == 0)
{
return(null);
}
Dictionary <string, string> attValues = new Dictionary <string, string>();
typeId = H5D.get_type(datasetId);
H5T.class_t type = H5T.get_class(typeId);
IntPtr tSize = H5T.get_size(typeId);
spaceId = H5D.get_space(datasetId);
int length = H5S.get_simple_extent_ndims(spaceId);
ulong[] dims = new ulong[length];
H5S.get_simple_extent_dims(spaceId, dims, null);
ulong storageSize = H5D.get_storage_size(datasetId);
attValues.Add("DataSetName", datasetName);
attValues.Add("DataType", type.ToString());
attValues.Add("DataTypeSize", tSize.ToString() + "Byte");
attValues.Add("Dims", String.Join("*", dims));
attValues.Add("StorageSize", storageSize.ToString() + "Byte");
//所有Attributes的键
ArrayList arrayList = new ArrayList();
GCHandle handle = GCHandle.Alloc(arrayList);
ulong n = 0;
// the callback is defined in H5ATest.cs
H5A.operator_t cb = (int location_id, IntPtr attr_name, ref H5A.info_t ainfo, IntPtr op_data) =>
{
GCHandle hnd = (GCHandle)op_data;
ArrayList al = (hnd.Target as ArrayList);
int len = 0;
while (Marshal.ReadByte(attr_name, len) != 0)
{
++len;
}
byte[] buf = new byte[len];
Marshal.Copy(attr_name, buf, 0, len);
al.Add(Encoding.UTF8.GetString(buf));
return(0);
};
H5A.iterate(datasetId, H5.index_t.NAME, H5.iter_order_t.NATIVE, ref n, cb, (IntPtr)handle);
handle.Free();
foreach (string attName in arrayList)
{
attValues.Add(attName, ReadAttributeValue(datasetId, attName));
}
return(attValues);
}
finally
{
if (spaceId != 0)
{
H5S.close(spaceId);
}
if (typeId != 0)
{
H5T.close(typeId);
}
if (datasetId != 0)
{
H5D.close(datasetId);
}
if (groupId != 0)
{
H5G.close(groupId);
}
}
}
private object GetAttributeValue(int _h5FileId, string attributeName)
{
H5AttributeId attId = H5A.open(_h5FileId, attributeName);
if (attId == 0)
{
return(null);
}
H5DataTypeId typeId = 0;
H5DataTypeId dtId = 0;
H5A.info_t attInfo = new H5A.info_t();
H5DataSpaceId spaceId = 0;
H5DataTypeId oldTypeId = 0;
object retObject = null;
try
{
typeId = H5A.get_type(attId);
H5A.get_info(attId, ref attInfo);
dtId = H5A.get_type(attId);
spaceId = H5A.get_space(attId);
IntPtr dataSize = H5T.get_size(dtId);
//
oldTypeId = typeId;
typeId = H5T.get_native_type(typeId, H5T.direction_t.DEFAULT);
H5T.class_t typeClass = H5T.get_class(typeId);
int ndims = H5S.get_simple_extent_ndims(spaceId);
ulong[] dims = new ulong[ndims];
H5S.get_simple_extent_dims(spaceId, dims, null);
ulong dimSize = 1;
if (dims.Length == 0)
{
dimSize = 1;
}
else
{
foreach (ulong dim in dims)
{
dimSize *= dim;
}
}
switch (typeClass)
{
case H5T.class_t.NO_CLASS:
break;
case H5T.class_t.INTEGER:
// H5T.Sign.TWOS_COMPLEMENT;
H5T.sign_t sign = H5T.get_sign(oldTypeId);
switch (dataSize.ToInt32())
{
case 1:
retObject = ReadArray <byte>(dimSize, attId, typeId);
break;
case 2:
switch (sign)
{
case H5T.sign_t.SGN_2:
retObject = ReadArray <Int16>(dimSize, attId, typeId);
break;
case H5T.sign_t.NONE:
retObject = ReadArray <UInt16>(dimSize, attId, typeId);
break;
}
break;
case 4:
switch (sign)
{
case H5T.sign_t.SGN_2:
retObject = ReadArray <Int32>(dimSize, attId, typeId);
break;
case H5T.sign_t.NONE:
retObject = ReadArray <UInt32>(dimSize, attId, typeId);
break;
}
break;
case 8:
switch (sign)
{
case H5T.sign_t.SGN_2:
retObject = ReadArray <Int64>(dimSize, attId, typeId);
break;
case H5T.sign_t.NONE:
retObject = ReadArray <UInt64>(dimSize, attId, typeId);
break;
}
break;
}
break;
case H5T.class_t.FLOAT:
switch (dataSize.ToInt32())
{
case 4:
retObject = ReadArray <float>(dimSize, attId, typeId);
break;
case 8:
retObject = ReadArray <double>(dimSize, attId, typeId);
break;
}
break;
case H5T.class_t.STRING:
ulong size = attInfo.data_size;
byte[] chars = ReadArray <byte>(size, attId, typeId);
retObject = Encoding.ASCII.GetString(chars);
break;
default:
break;
}
return(retObject);
}
finally
{
if (spaceId != 0)
{
H5S.close(spaceId);
}
if (attId != 0)
{
H5A.close(attId);
}
if (oldTypeId != 0)
{
H5T.close(oldTypeId);
}
if (typeId != 0)
{
H5T.close(typeId);
}
if (dtId != 0)
{
H5T.close(dtId);
}
}
}
private int depth_first(HObject parentObject, int nTotal)
{
Hdf5Utils.LogInfo?.Invoke($"depth_first({parentObject}): start");
int nelems;
string fullPath = null;
string ppath = null;
long gid = -1;
H5Group pgroup = (H5Group)parentObject;
ppath = pgroup.getPath();
if (ppath == null)
{
fullPath = HObject.SEPARATOR;
}
else
{
fullPath = ppath + pgroup.getName() + HObject.SEPARATOR;
}
nelems = 0;
try
{
gid = pgroup.open();
var info = new H5G.info_t();
H5G.get_info(gid, ref info);
nelems = (int)info.nlinks;
}
catch (Exception ex)
{
nelems = -1;
Hdf5Utils.LogError?.Invoke($"depth_first({parentObject}): H5Gget_info(gid {gid}) failure: {ex}");
}
if (nelems <= 0)
{
pgroup.close(gid);
Hdf5Utils.LogInfo?.Invoke($"depth_first({parentObject}): nelems <= 0");
Hdf5Utils.LogInfo?.Invoke($"depth_first({parentObject}): finish");
return(nTotal);
}
// since each call of H5.H5Gget_objname_by_idx() takes about one second.
// 1,000,000 calls take 12 days. Instead of calling it in a loop,
// we use only one call to get all the information, which takes about
// two seconds
int[] objTypes = new int[nelems];
//long[] fNos = new long[nelems];
//long[] objRefs = new long[nelems];
string[] objNames = new string[nelems];
H5L.info_t[] infos = new H5L.info_t[nelems];
try
{
int i = 0;
int callback(long group, IntPtr name, ref H5L.info_t info, IntPtr op_data)
{
string realName = Marshal.PtrToStringAuto(name);
objTypes[i] = (int)info.type;
objNames[i] = realName;
infos[i] = info;
return(i++);
}
ulong pos = 0;
H5L.iterate(gid, indexType, indexOrder, ref pos, callback, IntPtr.Zero);
//for (ulong i = 0; i < (ulong)nelems; i++)
//{
// H5G.info_t info = new H5G.info_t();
// H5G.get_info_by_idx(fid, fullPath, indexType, indexOrder, i, ref info);
// infos[i] = info;
//}
// H5.H5Gget_obj_info_full(fid, fullPath, objNames, objTypes, null, fNos, objRefs, indexType, indexOrder);
}
catch (Exception ex)
{
Hdf5Utils.LogError?.Invoke($"depth_first({parentObject}): failure: {ex}");
Hdf5Utils.LogError?.Invoke($"depth_first({parentObject}): finish");
return(nTotal);
}
int nStart = getStartMembers();
int nMax = getMaxMembers();
string obj_name;
int obj_type;
// Iterate through the file to see members of the group
for (int i = 0; i < nelems; i++)
{
obj_name = objNames[i];
obj_type = objTypes[i];
Hdf5Utils.LogInfo?.Invoke($"depth_first({parentObject}): obj_name={obj_name}, obj_type={obj_type}");
if (obj_name == null)
{
Hdf5Utils.LogInfo?.Invoke($"depth_first({parentObject}): continue after null obj_name");
continue;
}
nTotal++;
if (nMax > 0)
{
if ((nTotal - nStart) >= nMax)
{
break; // loaded enough objects
}
}
bool skipLoad = (nTotal > 0) && (nTotal < nStart);
// create a new group
if (obj_type == HDF5Constants.H5O_TYPE_GROUP)
{
H5Group g = new H5Group(this, obj_name, fullPath, pgroup);
pgroup.addToMemberList(g);
// detect and stop loops
// a loop is detected if there exists object with the same
// object ID by tracing path back up to the root.
bool hasLoop = false;
H5Group tmpObj = (H5Group)parentObject;
while (tmpObj != null)
{
if (tmpObj.equalsOID(new IntPtr((int)infos[i].u.address)) && (tmpObj.getPath() != null))
{
hasLoop = true;
break;
}
else
{
tmpObj = (H5Group)tmpObj.getParent();
}
}
// recursively go through the next group
// stops if it has loop.
if (!hasLoop)
{
nTotal = depth_first(g, nTotal);
}
}
else if (skipLoad)
{
continue;
}
else if (obj_type == HDF5Constants.H5O_TYPE_DATASET)
{
long did = -1;
long tid = -1;
H5T.class_t tclass = H5T.class_t.NO_CLASS;
try
{
did = H5D.open(fid, fullPath + obj_name, HDF5Constants.H5P_DEFAULT);
if (did >= 0)
{
tid = H5D.get_type(did);
tclass = H5T.get_class(tid);
if ((tclass == HDF5Constants.H5T_ARRAY) || (tclass == HDF5Constants.H5T_VLEN))
{
// for ARRAY, the type is determined by the base type
long btid = H5T.get_super(tid);
tclass = H5T.get_class(btid);
try
{
H5T.close(btid);
}
catch (Exception ex)
{
Hdf5Utils.LogInfo?.Invoke($"depth_first({parentObject})[{i}] dataset {obj_name} H5Tclose(btid {btid}) failure: {ex}");
}
}
}
else
{
Hdf5Utils.LogError?.Invoke($"depth_first({parentObject})[{i}] {obj_name} dataset open failure");
}
}
catch (Exception ex)
{
Hdf5Utils.LogError?.Invoke($"depth_first({parentObject})[{i}] {obj_name} dataset access failure: {ex}");
}
finally
{
try
{
H5T.close(tid);
}
catch (Exception ex)
{
Hdf5Utils.LogError?.Invoke($"depth_first({parentObject})[{i}] dataset {obj_name} H5Tclose(tid {tid}) failure: {ex}");
}
try
{
H5D.close(did);
}
catch (Exception ex)
{
Hdf5Utils.LogInfo?.Invoke($"depth_first({parentObject})[{i}] dataset {obj_name} H5Dclose(did {did}) failure: {ex}");
}
}
//todo:
//Dataset d = null;
//if (tclass == HDF5Constants.H5T_COMPOUND)
//{
// // create a new compound dataset
// d = new H5CompoundDS(this, obj_name, fullPath, oid); // deprecated!
//}
//else
//{
// // create a new scalar dataset
// d = new H5ScalarDS(this, obj_name, fullPath, oid); // deprecated!
//}
// pgroup.addToMemberList(d);
}
else if (obj_type == HDF5Constants.H5O_TYPE_NAMED_DATATYPE)
{
//Datatype t = new H5Datatype(this, obj_name, fullPath, oid); // deprecated!
//pgroup.addToMemberList(t);
}
else if (obj_type == HDF5Constants.H5O_TYPE_UNKNOWN)
{
//H5Link link = new H5Link(this, obj_name, fullPath, oid);
// pgroup.addToMemberList(link);
continue; // do the next one, if the object is not identified.
}
} // ( i = 0; i < nelems; i++)
pgroup.close(gid);
Hdf5Utils.LogInfo?.Invoke($"depth_first({parentObject}): finish");
return(nTotal);
}
