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);
}