private H5File(H5Context context,
H5NamedReference reference,
ObjectHeader header,
string absoluteFilePath,
bool deleteOnClose)
: base(context, reference, header)
{
this.Path = absoluteFilePath;
_deleteOnClose = deleteOnClose;
}
internal H5Group(H5File file, H5Context context, H5NamedReference reference, ObjectHeader header)
: base(context, reference, header)
{
_file = file;
}
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);
}
internal H5Group(H5File file, H5Context context, H5NamedReference reference)
: base(context, reference)
{
_file = file;
_scratchPad = reference.ScratchPad;
}
// Only for H5File constructor
internal H5Group(H5Context context, H5NamedReference reference, ObjectHeader header)
: base(context, reference, header)
{
//
}
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);
}
internal H5AttributableObject(H5Context context, H5NamedReference reference)
: base(context, reference)
{
//
}
internal H5AttributableObject(H5Context context, H5NamedReference reference, ObjectHeader header)
: base(context, reference, header)
{
//
}
internal H5Dataset(H5Context context, H5NamedReference reference, ObjectHeader header)
: base(context, reference, header)
{
foreach (var message in this.Header.HeaderMessages)
{
var type = message.Data.GetType();
if (typeof(DataLayoutMessage).IsAssignableFrom(type))
{
this.DataLayout = (DataLayoutMessage)message.Data;
}
else if (type == typeof(DataspaceMessage))
{
this.Dataspace = (DataspaceMessage)message.Data;
}
else if (type == typeof(DatatypeMessage))
{
this.Datatype = (DatatypeMessage)message.Data;
}
else if (type == typeof(FillValueMessage))
{
this.FillValue = (FillValueMessage)message.Data;
}
else if (type == typeof(FilterPipelineMessage))
{
this.FilterPipeline = (FilterPipelineMessage)message.Data;
}
else if (type == typeof(ObjectModificationMessage))
{
this.ObjectModification = (ObjectModificationMessage)message.Data;
}
else if (type == typeof(ExternalFileListMessage))
{
this.ExternalFileList = (ExternalFileListMessage)message.Data;
}
}
// check that required fields are set
if (this.DataLayout == null)
{
throw new Exception("The data layout message is missing.");
}
if (this.Dataspace == null)
{
throw new Exception("The dataspace message is missing.");
}
if (this.Datatype == null)
{
throw new Exception("The data type message is missing.");
}
if (this.FillValue == null)
{
throw new Exception("The fill value message is missing.");
}
}
internal H5Object(H5Context context, H5NamedReference reference, ObjectHeader header)
{
this.Context = context;
this.Reference = reference;
_header = header;
}
internal H5Object(H5Context context, H5NamedReference reference)
{
this.Context = context;
this.Reference = reference;
}
internal H5CommitedDatatype(H5Context context, ObjectHeader header, H5NamedReference reference)
: base(context, reference, header)
{
this.Datatype = header.GetMessage <DatatypeMessage>();
}
internal H5UnresolvedLink(H5NamedReference reference)
: base(default, reference)
{
this.Reason = reference.Exception;
}