internal H5NamedReference InternalGet(string path, H5LinkAccess linkAccess)
{
if (path == "/")
{
return(this.File.Reference);
}
var isRooted = path.StartsWith('/');
var segments = isRooted ? path.Split('/').Skip(1).ToArray() : path.Split('/');
var current = isRooted ? this.File.Reference : this.Reference;
for (int i = 0; i < segments.Length; i++)
{
var group = current.Dereference() as H5Group;
if (group == null)
{
throw new Exception($"Path segment '{segments[i - 1]}' is not a group.");
}
if (!group.TryGetReference(segments[i], linkAccess, out var reference))
{
throw new Exception($"Could not find part of the path '{path}'.");
}
current = reference;
}
return(current);
}
private bool InternalExists(string path, H5LinkAccess linkAccess)
{
if (path == "/")
{
return(true);
}
var isRooted = path.StartsWith('/');
var segments = isRooted ? path.Split('/').Skip(1).ToArray() : path.Split('/');
var current = isRooted ? this.File.Reference : this.Reference;
for (int i = 0; i < segments.Length; i++)
{
var group = current.Dereference() as H5Group;
if (group == null)
{
return(false);
}
if (!group.TryGetReference(segments[i], linkAccess, out var reference))
{
return(false);
}
current = reference;
}
return(true);
}
private H5NamedReference GetObjectReference(LinkMessage linkMessage, H5LinkAccess linkAccess)
{
return(linkMessage.LinkInfo switch
{
HardLinkInfo hard => new H5NamedReference(linkMessage.LinkName, hard.HeaderAddress, this.File),
SoftLinkInfo soft => new H5SymbolicLink(linkMessage, this).GetTarget(linkAccess),
ExternalLinkInfo external => new H5SymbolicLink(linkMessage, this).GetTarget(linkAccess),
_ => throw new Exception($"Unknown link type '{linkMessage.LinkType}'.")
});
public H5Object Get(H5ObjectReference reference, H5LinkAccess linkAccess = default)
{
if (this.Reference.Value == reference.Value)
{
return(this);
}
return(this
.InternalGet(reference, linkAccess)
.Dereference());
}
public H5Group Group(string path, H5LinkAccess linkAccess = default)
{
var link = this.Get(path, linkAccess);
var group = link as H5Group;
if (group == null)
{
throw new Exception($"The requested link exists but cannot be casted to {nameof(H5Group)} because it is of type {link.GetType().Name}.");
}
return(group);
}
public H5CommitedDatatype CommitedDatatype(string path, H5LinkAccess linkAccess = default)
{
var link = this.Get(path, linkAccess);
var castedLink = link as H5CommitedDatatype;
if (castedLink == null)
{
throw new Exception($"The requested link exists but cannot be casted to {nameof(H5CommitedDatatype)} because it is of type {link.GetType().Name}.");
}
return(castedLink);
}
internal H5NamedReference InternalGet(H5ObjectReference reference, H5LinkAccess linkAccess)
{
var alreadyVisted = new HashSet <ulong>();
if (this.TryGetReference(reference, alreadyVisted, linkAccess, recursionLevel: 0, out var namedReference))
{
return(namedReference);
}
else
{
throw new Exception($"Could not find object for reference with value '{reference.Value:X}'.");
}
}
public H5NamedReference GetTarget(H5LinkAccess linkAccess)
{
// this file
if (string.IsNullOrWhiteSpace(this.ObjectPath))
{
try
{
var reference = this.Parent.InternalGet(this.Value, linkAccess);
reference.Name = this.Name;
return(reference);
}
catch (Exception ex)
{
return(new H5NamedReference(this.Name, Superblock.UndefinedAddress)
{
Exception = ex
});
}
}
// external file
else
{
try
{
var absoluteFilePath = H5Utils.ConstructExternalFilePath(this.Parent.File, this.Value, linkAccess);
var objectPath = this.ObjectPath;
var externalFile = H5Cache.GetH5File(this.Parent.Context.Superblock, absoluteFilePath);
return(externalFile.InternalGet(objectPath, linkAccess));
}
catch (Exception ex)
{
return(new H5NamedReference(this.Name, Superblock.UndefinedAddress)
{
Exception = ex
});
}
}
}
public H5Object Get(string path, H5LinkAccess linkAccess = default)
{
return(this
.InternalGet(path, linkAccess)
.Dereference());
}
public bool Exists(string path, H5LinkAccess linkAccess = default)
{
return(this.InternalExists(path, linkAccess));
}
private IEnumerable <H5NamedReference> EnumerateReferences(H5LinkAccess linkAccess)
{
// https://support.hdfgroup.org/HDF5/doc/RM/RM_H5G.html
// section "Group implementations in HDF5"
/* cached data */
if (_scratchPad != null)
{
var localHeap = _scratchPad.LocalHeap;
var references = this
.EnumerateSymbolTableNodes(_scratchPad.GetBTree1(this.DecodeGroupKey))
.SelectMany(node => node.GroupEntries
.Select(entry => this.GetObjectReferencesForSymbolTableEntry(localHeap, entry, linkAccess)));
foreach (var reference in references)
{
yield return(reference);
}
}
else
{
var symbolTableHeaderMessages = this.Header.GetMessages <SymbolTableMessage>();
if (symbolTableHeaderMessages.Any())
{
/* Original approach.
* IV.A.2.r.: The Symbol Table Message
* Required for "old style" groups; may not be repeated. */
if (symbolTableHeaderMessages.Count() != 1)
{
throw new Exception("There may be only a single symbol table header message.");
}
var smessage = symbolTableHeaderMessages.First();
var localHeap = smessage.LocalHeap;
var references = this
.EnumerateSymbolTableNodes(smessage.GetBTree1(this.DecodeGroupKey))
.SelectMany(node => node.GroupEntries
.Select(entry => this.GetObjectReferencesForSymbolTableEntry(localHeap, entry, linkAccess)));
foreach (var reference in references)
{
yield return(reference);
}
}
else
{
var linkInfoMessages = this.Header.GetMessages <LinkInfoMessage>();
if (linkInfoMessages.Any())
{
IEnumerable <LinkMessage> linkMessages;
if (linkInfoMessages.Count() != 1)
{
throw new Exception("There may be only a single link info message.");
}
var lmessage = linkInfoMessages.First();
/* New (1.8) indexed format (in combination with Group Info Message)
* IV.A.2.c. The Link Info Message
* Optional; may not be repeated. */
if (!this.Context.Superblock.IsUndefinedAddress(lmessage.BTree2NameIndexAddress))
{
linkMessages = this.EnumerateLinkMessagesFromLinkInfoMessage(lmessage);
}
/* New (1.8) compact format
* IV.A.2.g. The Link Message
* A group is storing its links compactly when the fractal heap address
* in the Link Info Message is set to the "undefined address" value. */
else
{
linkMessages = this.Header.GetMessages <LinkMessage>();
}
// build links
foreach (var linkMessage in linkMessages)
{
yield return(this.GetObjectReference(linkMessage, linkAccess));
}
}
else
{
throw new Exception("No link information found in object header.");
}
}
}
}
internal bool TryGetReference(H5ObjectReference reference, HashSet <ulong> alreadyVisited, H5LinkAccess linkAccess, int recursionLevel, out H5NamedReference namedReference)
{
// similar to H5Gint.c (H5G_visit)
if (recursionLevel >= 100)
{
throw new Exception("Too much recursion.");
}
bool skip = false;
namedReference = default;
/* If its ref count is > 1, we add it to the list of visited objects
* (because it could come up again during traversal) */
if (this.ReferenceCount > 1)
{
if (alreadyVisited.Contains(this.Reference.Value))
{
skip = true;
}
else
{
alreadyVisited.Add(this.Reference.Value);
}
}
if (!skip)
{
var references = this
.EnumerateReferences(linkAccess)
.ToList();
namedReference = references
.FirstOrDefault(current => current.Value == reference.Value);
if (namedReference.Name != null /* if struct value is not equal to default */)
{
return(true);
}
else
{
// search childs for reference
foreach (var childReference in references)
{
var group = childReference.Dereference() as H5Group;
if (group != null)
{
if (group.TryGetReference(reference, alreadyVisited, linkAccess, recursionLevel + 1, out namedReference))
{
return(true);
}
}
}
}
}
return(false);
}
private bool TryGetReference(string name, H5LinkAccess linkAccess, out H5NamedReference namedReference)
{
namedReference = default;
/* cached data */
if (_scratchPad != null)
{
var localHeap = _scratchPad.LocalHeap;
this.Context.Reader.Seek((long)_scratchPad.BTree1Address, SeekOrigin.Begin);
var tree = new BTree1Node <BTree1GroupKey>(this.Context.Reader, this.Context.Superblock, this.DecodeGroupKey);
var b = tree.EnumerateNodes().ToList();
this.Context.Reader.Seek((long)_scratchPad.NameHeapAddress, SeekOrigin.Begin);
var heap = new LocalHeap(this.Context.Reader, this.Context.Superblock);
var c = heap.GetObjectName(0);
var success = _scratchPad
.GetBTree1(this.DecodeGroupKey)
.TryFindUserData(out var userData,
(leftKey, rightKey) => this.NodeCompare3(localHeap, name, leftKey, rightKey),
(ulong address, out BTree1SymbolTableUserData userData) => this.NodeFound(localHeap, name, address, out userData));
if (success)
{
namedReference = this.GetObjectReferencesForSymbolTableEntry(localHeap, userData.SymbolTableEntry, linkAccess);
return(true);
}
}
else
{
var symbolTableHeaderMessages = this.Header.GetMessages <SymbolTableMessage>();
if (symbolTableHeaderMessages.Any())
{
/* Original approach.
* IV.A.2.r.: The Symbol Table Message
* Required for "old style" groups; may not be repeated. */
if (symbolTableHeaderMessages.Count() != 1)
{
throw new Exception("There may be only a single symbol table header message.");
}
var smessage = symbolTableHeaderMessages.First();
var localHeap = smessage.LocalHeap;
var success = smessage
.GetBTree1(this.DecodeGroupKey)
.TryFindUserData(out var userData,
(leftKey, rightKey) => this.NodeCompare3(localHeap, name, leftKey, rightKey),
(ulong address, out BTree1SymbolTableUserData userData) => this.NodeFound(localHeap, name, address, out userData));
if (success)
{
namedReference = this.GetObjectReferencesForSymbolTableEntry(localHeap, userData.SymbolTableEntry, linkAccess);
return(true);
}
}
else
{
var linkInfoMessages = this.Header.GetMessages <LinkInfoMessage>();
if (linkInfoMessages.Any())
{
if (linkInfoMessages.Count() != 1)
{
throw new Exception("There may be only a single link info message.");
}
var lmessage = linkInfoMessages.First();
/* New (1.8) indexed format (in combination with Group Info Message)
* IV.A.2.c. The Link Info Message
* Optional; may not be repeated. */
if (!this.Context.Superblock.IsUndefinedAddress(lmessage.BTree2NameIndexAddress))
{
if (this.TryGetLinkMessageFromLinkInfoMessage(lmessage, name, out var linkMessage))
{
namedReference = this.GetObjectReference(linkMessage, linkAccess);
return(true);
}
}
/* New (1.8) compact format
* IV.A.2.g. The Link Message
* A group is storing its links compactly when the fractal heap address
* in the Link Info Message is set to the "undefined address" value. */
else
{
var linkMessage = this.Header
.GetMessages <LinkMessage>()
.FirstOrDefault(message => message.LinkName == name);
if (linkMessage != null)
{
namedReference = this.GetObjectReference(linkMessage, linkAccess);
return(true);
}
}
}
else
{
throw new Exception("No link information found in object header.");
}
}
}
return(false);
}
public IEnumerable <H5Object> GetChildren(H5LinkAccess linkAccess = default)
{
return(this
.EnumerateReferences(linkAccess)
.Select(reference => reference.Dereference()));
}
