Creation order enumeration and other changes

src/PureHDF/VOL/Native/API.Reading/NativeGroup.cs

@@ -131,6 +131,27 @@ public IEnumerable<IH5Object> Children(H5LinkAccess linkAccess = default)
             .Select(reference => reference.Dereference());
     }
 
+    /// <summary>
+    /// Gets the number of children in this group without dereferencing them.
+    /// </summary>
+    /// <returns>The number of children in this group.</returns>
+    public ulong GetChildCount()
+    {
+        var linkInfoMessage = GetLinkInfoMessage();
+
+        if (!Context.Superblock.IsUndefinedAddress(linkInfoMessage.BTree2NameIndexAddress))
+        {
+            return linkInfoMessage.BTree2NameIndex.RootNodePointer.TotalRecordCount;
+        }
+
+        if (Context.Superblock.IsUndefinedAddress(linkInfoMessage.FractalHeapAddress))
+        {
+            return (ulong)Header.GetMessages<LinkMessage>().Count();
+        }
+
+        throw new NotSupportedException("The group does not use compact or indexed dense link storage.");
+    }
+
     private bool InternalLinkExists(string path, H5LinkAccess linkAccess)
     {
         if (path == "/")
@@ -430,8 +451,16 @@ private IEnumerable<NativeNamedReference> EnumerateReferences(H5LinkAccess linkA
                      * 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 = Header.GetMessages<LinkMessage>();
 
+                        if (lmessage.Flags.HasFlag(CreationOrderFlags.TrackCreationOrder))
+                        {
+                            linkMessages = linkMessages
+                                .OrderBy(message => message.CreationOrder);
+                        }
+                    }
+
                     // build links
                     foreach (var linkMessage in linkMessages)
                     {
@@ -451,29 +480,73 @@ private IEnumerable<NativeNamedReference> EnumerateReferences(H5LinkAccess linkA
     #region Link Message
 
     private IEnumerable<LinkMessage> EnumerateLinkMessagesFromLinkInfoMessage(LinkInfoMessage infoMessage)
+    {
+        if (infoMessage.Flags.HasFlag(CreationOrderFlags.TrackCreationOrder))
+            return EnumerateLinkMessagesByCreationOrder(infoMessage);
+
+        return EnumerateLinkMessagesByName(infoMessage);
+    }
+
+    private IEnumerable<LinkMessage> EnumerateLinkMessagesByName(LinkInfoMessage infoMessage)
     {
         var fractalHeap = infoMessage.FractalHeap;
         var btree2NameIndex = infoMessage.BTree2NameIndex;
-        var records = btree2NameIndex
-            .EnumerateRecords()
-            .ToList();
 
         // local cache: indirectly accessed, non-filtered
-        List<BTree2Record01>? record01Cache = null;
+        BTree2Header<BTree2Record01>? record01Cache = null;
+
+        foreach (var record in btree2NameIndex.EnumerateRecords())
+        {
+            yield return ReadLinkMessage(fractalHeap, record.HeapId, ref record01Cache);
+        }
+    }
 
-        foreach (var record in records)
+    private IEnumerable<LinkMessage> EnumerateLinkMessagesByCreationOrder(LinkInfoMessage infoMessage)
+    {
+        if (Context.Superblock.IsUndefinedAddress(infoMessage.BTree2CreationOrderIndexAddress))
         {
-            using var localDriver = new H5StreamDriver(new MemoryStream(record.HeapId), leaveOpen: false);
-            var heapId = FractalHeapId.Construct(Context, localDriver, fractalHeap);
+            return EnumerateLinkMessagesByName(infoMessage)
+                .OrderBy(message => message.CreationOrder);
+        }
 
-            yield return heapId.Read(driver =>
-            {
-                var message = LinkMessage.Decode(Context);
-                return message;
-            }, ref record01Cache);
+        return EnumerateLinkMessagesByCreationOrderIndex(infoMessage);
+    }
+
+    private IEnumerable<LinkMessage> EnumerateLinkMessagesByCreationOrderIndex(LinkInfoMessage infoMessage)
+    {
+        var fractalHeap = infoMessage.FractalHeap;
+        var btree2CreationOrder = infoMessage.BTree2CreationOrder;
+
+        // local cache: indirectly accessed, non-filtered
+        BTree2Header<BTree2Record01>? record01Cache = null;
+
+        foreach (var record in btree2CreationOrder.EnumerateRecords())
+        {
+            yield return ReadLinkMessage(fractalHeap, record.HeapId, ref record01Cache);
         }
     }
 
+    private LinkInfoMessage GetLinkInfoMessage()
+    {
+        var linkInfoMessages = Header.GetMessages<LinkInfoMessage>();
+
+        if (!linkInfoMessages.Any())
+            throw new Exception("No link information found in object header.");
+
+        if (linkInfoMessages.Count() != 1)
+            throw new Exception("There may be only a single link info message.");
+
+        return linkInfoMessages.First();
+    }
+
+    private LinkMessage ReadLinkMessage(FractalHeapHeader fractalHeap, byte[] heapIdBytes, ref BTree2Header<BTree2Record01>? record01Cache)
+    {
+        using var localDriver = new H5StreamDriver(new MemoryStream(heapIdBytes), leaveOpen: false);
+        var heapId = FractalHeapId.Construct(Context, localDriver, fractalHeap);
+
+        return heapId.Read(driver => LinkMessage.Decode(Context), ref record01Cache);
+    }
+
     private bool TryGetLinkMessageFromLinkInfoMessage(LinkInfoMessage linkInfoMessage,
                                                       string name,
                                                       [NotNullWhen(returnValue: true)] out LinkMessage? linkMessage)

src/PureHDF/VOL/Native/API.Reading/NativeObject.cs

@@ -186,16 +186,13 @@ private IEnumerable<AttributeMessage> EnumerateAttributeMessagesFromAttributeInf
         AttributeInfoMessage attributeInfoMessage)
     {
         var btree2NameIndex = attributeInfoMessage.BTree2NameIndex;
-        var records = btree2NameIndex
-            .EnumerateRecords()
-            .ToList();
 
         var fractalHeap = attributeInfoMessage.FractalHeap;
 
         // local cache: indirectly accessed, non-filtered
-        List<BTree2Record01>? record01Cache = null;
+        BTree2Header<BTree2Record01>? record01Cache = null;
 
-        foreach (var record in records)
+        foreach (var record in btree2NameIndex.EnumerateRecords())
         {
             // TODO: duplicate1_of_3
             using var localDriver = new H5StreamDriver(new MemoryStream(record.HeapId), leaveOpen: false);

src/PureHDF/VOL/Native/Core.Reading/NativeCache.cs

@@ -8,8 +8,8 @@ internal static class NativeCache
 
     static NativeCache()
     {
-        _globalHeapMap = new ConcurrentDictionary<H5DriverBase, Dictionary<ulong, GlobalHeapCollection>>();
-        _fileMap = new ConcurrentDictionary<H5DriverBase, Dictionary<string, NativeFile>>();
+        _globalHeapMap = new ConcurrentDictionary<H5DriverBase, ConcurrentDictionary<ulong, GlobalHeapCollection>>();
+        _fileMap = new ConcurrentDictionary<H5DriverBase, ConcurrentDictionary<string, NativeFile>>();
     }
 
     #endregion
@@ -41,7 +41,7 @@ public static void Clear(H5DriverBase driver)
 
     #region Global Heap
 
-    private static readonly ConcurrentDictionary<H5DriverBase, Dictionary<ulong, GlobalHeapCollection>> _globalHeapMap;
+    private static readonly ConcurrentDictionary<H5DriverBase, ConcurrentDictionary<ulong, GlobalHeapCollection>> _globalHeapMap;
 
     public static GlobalHeapCollection GetGlobalHeapObject(
         NativeReadContext context,
@@ -50,8 +50,8 @@ public static GlobalHeapCollection GetGlobalHeapObject(
     {
         if (!_globalHeapMap.TryGetValue(context.Driver, out var addressToCollectionMap))
         {
-            addressToCollectionMap = new Dictionary<ulong, GlobalHeapCollection>();
-            _globalHeapMap.AddOrUpdate(context.Driver, addressToCollectionMap, (_, oldAddressToCollectionMap) => addressToCollectionMap);
+            addressToCollectionMap = new ConcurrentDictionary<ulong, GlobalHeapCollection>();
+            _globalHeapMap.AddOrUpdate(context.Driver, addressToCollectionMap, (_, oldAddressToCollectionMap) => oldAddressToCollectionMap);
         }
 
         if (!addressToCollectionMap.TryGetValue(address, out var collection))
@@ -74,7 +74,7 @@ public static GlobalHeapCollection GetGlobalHeapObject(
 
     #region File Handles
 
-    private static readonly ConcurrentDictionary<H5DriverBase, Dictionary<string, NativeFile>> _fileMap;
+    private static readonly ConcurrentDictionary<H5DriverBase, ConcurrentDictionary<string, NativeFile>> _fileMap;
 
     public static NativeFile GetNativeFile(H5DriverBase driver, string absoluteFilePath)
     {
@@ -86,8 +86,8 @@ public static NativeFile GetNativeFile(H5DriverBase driver, string absoluteFileP
 
         if (!_fileMap.TryGetValue(driver, out var pathToNativeFileMap))
         {
-            pathToNativeFileMap = new Dictionary<string, NativeFile>();
-            _fileMap.AddOrUpdate(driver, pathToNativeFileMap, (_, oldPathToNativeFileMap) => pathToNativeFileMap);
+            pathToNativeFileMap = new ConcurrentDictionary<string, NativeFile>();
+            _fileMap.AddOrUpdate(driver, pathToNativeFileMap, (_, oldPathToNativeFileMap) => oldPathToNativeFileMap);
         }
 
         if (!pathToNativeFileMap.TryGetValue(uri.AbsoluteUri, out var nativeFile))

src/PureHDF/VOL/Native/FileFormat/Level1/BTree2/BTree2Header.cs

@@ -283,7 +283,7 @@ public IEnumerable<T> EnumerateRecords()
             return EnumerateRecords(rootNode, Depth);
 
         else
-            return new List<T>();
+            return Enumerable.Empty<T>();
     }
 
     private IEnumerable<T> EnumerateRecords(BTree2Node<T> node, ushort nodeLevel)
@@ -296,18 +296,12 @@ private IEnumerable<T> EnumerateRecords(BTree2Node<T> node, ushort nodeLevel)
 
         if (internalNode is not null)
         {
-            var records = node.Records
-                .Cast<T>()
-                .ToList();
+            var records = internalNode.Records;
 
             var nodePointers = internalNode.NodePointers;
 
             for (int i = 0; i < nodePointers.Length; i++)
             {
-                // there is one more node pointer than records
-                if (i < records.Count)
-                    yield return records[i];
-
                 var nodePointer = nodePointers[i];
                 Context.Driver.SeekRelativeToBaseAddress((long)nodePointer.Address);
                 var childNodeLevel = (ushort)(nodeLevel - 1);
@@ -341,6 +335,10 @@ private IEnumerable<T> EnumerateRecords(BTree2Node<T> node, ushort nodeLevel)
                 {
                     yield return record;
                 }
+
+                // there is one more node pointer than records
+                if (i < records.Length)
+                    yield return records[i];
             }
         }
         // leaf node

src/PureHDF/VOL/Native/FileFormat/Level1/FractalHeap/FractalHeapId/FractalHeapId.cs

@@ -50,11 +50,11 @@ internal static FractalHeapId Construct(
     public T Read<T>(Func<H5DriverBase, T> func)
     {
         // TODO: Is there a better way?
-        List<BTree2Record01>? cache = null;
+        BTree2Header<BTree2Record01>? cache = null;
         return Read(func, ref cache);
     }
 
     public abstract T Read<T>(
         Func<H5DriverBase, T> func,
-        [AllowNull] ref List<BTree2Record01> record01Cache);
+        [AllowNull] ref BTree2Header<BTree2Record01> record01Cache);
 }

src/PureHDF/VOL/Native/FileFormat/Level1/FractalHeap/FractalHeapId/HugeObjectsFractalHeapIdSubType1.cs

@@ -23,19 +23,22 @@ internal static HugeObjectsFractalHeapIdSubType1 Decode(
 
     public override T Read<T>(
         Func<H5DriverBase, T> func,
-        [AllowNull] ref List<BTree2Record01> record01Cache)
+        [AllowNull] ref BTree2Header<BTree2Record01> record01Cache)
     {
         var driver = Context.Driver;
 
         // huge objects b-tree v2
         if (record01Cache is null)
         {
             driver.SeekRelativeToBaseAddress((long)HeapHeader.HugeObjectsBTree2Address);
-            var hugeBtree2 = BTree2Header<BTree2Record01>.Decode(Context, DecodeRecord01);
-            record01Cache = hugeBtree2.EnumerateRecords().ToList();
+            record01Cache = BTree2Header<BTree2Record01>.Decode(Context, DecodeRecord01);
         }
 
-        var hugeRecord = record01Cache.FirstOrDefault(record => record.HugeObjectId == BTree2Key);
+        var success = record01Cache.TryFindRecord(out var hugeRecord, record => BTree2Key.CompareTo(record.HugeObjectId));
+
+        if (!success)
+            throw new Exception("Could not find huge fractal heap object.");
+
         driver.SeekRelativeToBaseAddress((long)hugeRecord.HugeObjectAddress);
 
         return func(driver);

src/PureHDF/VOL/Native/FileFormat/Level1/FractalHeap/FractalHeapId/HugeObjectsFractalHeapIdSubType2.cs

@@ -22,7 +22,7 @@ ulong BTree2Key
 
     public override T Read<T>(
         Func<H5DriverBase, T> func,
-        [AllowNull] ref List<BTree2Record01> record01Cache)
+        [AllowNull] ref BTree2Header<BTree2Record01> record01Cache)
     {
         throw new Exception("Filtered data is not yet supported.");
     }

src/PureHDF/VOL/Native/FileFormat/Level1/FractalHeap/FractalHeapId/HugeObjectsFractalHeapIdSubType3.cs

@@ -20,7 +20,7 @@ public static HugeObjectsFractalHeapIdSubType3 Decode(NativeReadContext context,
     }
     public override T Read<T>(
         Func<H5DriverBase, T> func,
-        [AllowNull] ref List<BTree2Record01> record01Cache)
+        [AllowNull] ref BTree2Header<BTree2Record01> record01Cache)
     {
         Driver.SeekRelativeToBaseAddress((long)Address);
         return func(Driver);

src/PureHDF/VOL/Native/FileFormat/Level1/FractalHeap/FractalHeapId/HugeObjectsFractalHeapIdSubType4.cs

@@ -23,7 +23,7 @@ public static HugeObjectsFractalHeapIdSubType4 Decode(
 
     public override T Read<T>(
         Func<H5DriverBase, T> func,
-        [AllowNull] ref List<BTree2Record01> record01Cache)
+        [AllowNull] ref BTree2Header<BTree2Record01> record01Cache)
     {
         throw new Exception("Filtered data is not yet supported.");
     }

src/PureHDF/VOL/Native/FileFormat/Level1/FractalHeap/FractalHeapId/ManagedObjectsFractalHeapId.cs

@@ -26,7 +26,7 @@ public static ManagedObjectsFractalHeapId Decode(
 
     public override T Read<T>(
         Func<H5DriverBase, T> func,
-        [AllowNull] ref List<BTree2Record01> record01Cache)
+        [AllowNull] ref BTree2Header<BTree2Record01> record01Cache)
     {
         var address = Header.GetAddress(this);
 

src/PureHDF/VOL/Native/FileFormat/Level1/FractalHeap/FractalHeapId/TinyObjectsFractalHeapIdSubType1.cs

@@ -19,7 +19,7 @@ public static TinyObjectsFractalHeapIdSubType1 Decode(
 
     public override T Read<T>(
         Func<H5DriverBase, T> func,
-        [AllowNull] ref List<BTree2Record01> record01Cache)
+        [AllowNull] ref BTree2Header<BTree2Record01> record01Cache)
     {
         using var driver = new H5StreamDriver(new MemoryStream(Data), leaveOpen: false);
         return func.Invoke(driver);