private DataBlockElement[] ReadExtensibleArrayDataBlock(ExtensibleArrayHeader header, uint chunkSizeLength, uint elementIndex)
{
var secondaryBlockIndex = header.ComputeSecondaryBlockIndex(elementIndex + header.IndexBlockElementsCount);
var elementsCount = header.SecondaryBlockInfos[secondaryBlockIndex].ElementsCount;
var dataBlock = new ExtensibleArrayDataBlock(this.Context.Reader,
this.Context.Superblock,
header,
chunkSizeLength,
elementsCount);
if (dataBlock.PageCount > 0)
{
var pages = new List <DataBlockPage>((int)dataBlock.PageCount);
for (int i = 0; i < (int)dataBlock.PageCount; i++)
{
var page = new DataBlockPage(this.Context.Reader,
this.Context.Superblock,
header.DataBlockPageElementsCount,
dataBlock.ClientID,
chunkSizeLength);
pages.Add(page);
}
return(pages
.SelectMany(page => page.Elements)
.ToArray());
}
else
{
return(dataBlock.Elements);
}
}
// for later: H5EA__lookup_elmt
private void ReadExtensibleArray(Span <byte> buffer, ulong chunkSize)
{
var chunkSizeLength = this.ComputeChunkSizeLength(chunkSize);
var header = new ExtensibleArrayHeader(this.Context.Reader, this.Context.Superblock, chunkSizeLength);
var indexBlock = header.IndexBlock;
var elementIndex = 0U;
var elements = new List <DataBlockElement>()
.AsEnumerable();
// elements
elements = elements.Concat(indexBlock.Elements);
// data blocks
ReadDataBlocks(indexBlock.DataBlockAddresses);
// secondary blocks
#warning Is there any precalculated way to avoid checking all addresses?
var addresses = indexBlock
.SecondaryBlockAddresses
.Where(address => !this.Context.Superblock.IsUndefinedAddress(address));
foreach (var secondaryBlockAddress in addresses)
{
this.Context.Reader.Seek((long)secondaryBlockAddress, SeekOrigin.Begin);
var secondaryBlockIndex = header.ComputeSecondaryBlockIndex(elementIndex + header.IndexBlockElementsCount);
var secondaryBlock = new ExtensibleArraySecondaryBlock(this.Context.Reader, this.Context.Superblock, header, secondaryBlockIndex);
ReadDataBlocks(secondaryBlock.DataBlockAddresses);
}
var offset = 0UL;
foreach (var element in elements)
{
// if page/element is initialized (see also datablock.PageBitmap)
#warning Is there any precalculated way to avoid checking all addresses?
if (element.Address > 0 && !this.Context.Superblock.IsUndefinedAddress(element.Address))
{
this.SeekSliceAndReadChunk(offset, chunkSize, element.ChunkSize, element.Address, buffer);
}
offset += chunkSize;
}
void ReadDataBlocks(ulong[] dataBlockAddresses)
{
#warning Is there any precalculated way to avoid checking all addresses?
dataBlockAddresses = dataBlockAddresses
.Where(address => !this.Context.Superblock.IsUndefinedAddress(address))
.ToArray();
foreach (var dataBlockAddress in dataBlockAddresses)
{
this.Context.Reader.Seek((long)dataBlockAddress, SeekOrigin.Begin);
var newElements = this.ReadExtensibleArrayDataBlock(header, chunkSizeLength, elementIndex);
elements = elements.Concat(newElements);
elementIndex += (uint)newElements.Length;
}
}
}
public ExtensibleArrayIndexBlock(
H5BinaryReader reader,
Superblock superblock,
ExtensibleArrayHeader header,
Func <H5BinaryReader, T> decode)
{
// H5EAiblock.c (H5EA__iblock_alloc)
this.SecondaryBlockDataBlockAddressCount = 2 * (ulong)Math.Log(header.SecondaryBlockMinimumDataBlockPointerCount, 2);
ulong dataBlockPointerCount = (ulong)(2 * (header.SecondaryBlockMinimumDataBlockPointerCount - 1));
ulong secondaryBlockPointerCount = header.SecondaryBlockCount - this.SecondaryBlockDataBlockAddressCount;
// signature
var signature = reader.ReadBytes(4);
H5Utils.ValidateSignature(signature, ExtensibleArrayIndexBlock <T> .Signature);
// version
this.Version = reader.ReadByte();
// client ID
this.ClientID = (ClientID)reader.ReadByte();
// header address
this.HeaderAddress = superblock.ReadOffset(reader);
// elements
this.Elements = Enumerable
.Range(0, header.IndexBlockElementsCount)
.Select(i => decode(reader))
.ToArray();
// data block addresses
this.DataBlockAddresses = new ulong[dataBlockPointerCount];
for (ulong i = 0; i < dataBlockPointerCount; i++)
{
this.DataBlockAddresses[i] = superblock.ReadOffset(reader);
}
// secondary block addresses
this.SecondaryBlockAddresses = new ulong[secondaryBlockPointerCount];
for (ulong i = 0; i < secondaryBlockPointerCount; i++)
{
this.SecondaryBlockAddresses[i] = superblock.ReadOffset(reader);
}
// checksum
this.Checksum = reader.ReadUInt32();
}
public ExtensibleArraySecondaryBlock(H5BinaryReader reader, Superblock superblock, ExtensibleArrayHeader header, uint index)
{
// H5EAsblock.c (H5EA__sblock_alloc)
/* Compute/cache information */
var dataBlocksCount = header.SecondaryBlockInfos[index].DataBlockCount;
var elementsCount = header.SecondaryBlockInfos[index].ElementsCount;
var dataBlockPageCount = 0UL;
var dataBlockPageInitBitMaskSize = 0UL;
/* Check if # of elements in data blocks requires paging */
if (elementsCount > header.DataBlockPageElementsCount)
{
/* Compute # of pages in each data block from this super block */
dataBlockPageCount = elementsCount / header.DataBlockPageElementsCount;
/* Sanity check that we have at least 2 pages in data block */
if (dataBlockPageCount < 2)
{
throw new Exception("There must be at least two pages in the data block.");
}
/* Compute size of buffer for each data block's 'page init' bitmask */
dataBlockPageInitBitMaskSize = dataBlockPageCount + 7 / 8;
}
// signature
var signature = reader.ReadBytes(4);
H5Utils.ValidateSignature(signature, ExtensibleArraySecondaryBlock.Signature);
// version
this.Version = reader.ReadByte();
// client ID
this.ClientID = (ClientID)reader.ReadByte();
// header address
this.HeaderAddress = superblock.ReadOffset(reader);
// block offset
this.BlockOffset = H5Utils.ReadUlong(reader, header.ArrayOffsetsSize);
// page bitmap
// H5EAcache.c (H5EA__cache_sblock_deserialize)
/* Check for 'page init' bitmasks for this super block */
if (dataBlockPageCount > 0)
{
/* Compute total size of 'page init' buffer */
var totalPageInitSize = dataBlocksCount * dataBlockPageInitBitMaskSize;
/* Retrieve the 'page init' bitmasks */
this.PageBitmap = reader.ReadBytes((int)totalPageInitSize);
}
// data block addresses
this.DataBlockAddresses = new ulong[dataBlocksCount];
for (ulong i = 0; i < dataBlocksCount; i++)
{
this.DataBlockAddresses[i] = superblock.ReadOffset(reader);
}
// checksum
this.Checksum = reader.ReadUInt32();
}
public ExtensibleArrayIndexBlock(H5BinaryReader reader, Superblock superblock, ExtensibleArrayHeader header, uint chunkSizeLength)
{
// H5EAiblock.c (H5EA__iblock_alloc)
ulong secondaryBlockDataBlockAddressCount = 2 * (ulong)Math.Log(header.SecondaryBlockMinimumDataBlockPointerCount, 2);
ulong dataBlockPointerCount = (ulong)(2 * (header.SecondaryBlockMinimumDataBlockPointerCount - 1));
ulong secondaryBlockPointerCount = header.SecondaryBlockCount - secondaryBlockDataBlockAddressCount;
// signature
var signature = reader.ReadBytes(4);
H5Utils.ValidateSignature(signature, ExtensibleArrayIndexBlock.Signature);
// version
this.Version = reader.ReadByte();
// client ID
this.ClientID = (ClientID)reader.ReadByte();
// header address
this.HeaderAddress = superblock.ReadOffset(reader);
// elements
this.Elements = ArrayIndexUtils.ReadElements(reader, superblock, header.IndexBlockElementsCount, this.ClientID, chunkSizeLength);
// data block addresses
this.DataBlockAddresses = new ulong[dataBlockPointerCount];
for (ulong i = 0; i < dataBlockPointerCount; i++)
{
this.DataBlockAddresses[i] = superblock.ReadOffset(reader);
}
// secondary block addresses
this.SecondaryBlockAddresses = new ulong[secondaryBlockPointerCount];
for (ulong i = 0; i < secondaryBlockPointerCount; i++)
{
this.SecondaryBlockAddresses[i] = superblock.ReadOffset(reader);
}
// checksum
this.Checksum = reader.ReadUInt32();
}
public ExtensibleArrayDataBlock(H5BinaryReader reader, Superblock superblock, ExtensibleArrayHeader header, ulong elementCount, Func <H5BinaryReader, T> decode)
{
// H5EAdblock.c (H5EA__dblock_alloc)
this.PageCount = 0UL;
if (elementCount > header.DataBlockPageElementsCount)
{
/* Set the # of pages in the data block */
this.PageCount = elementCount / header.DataBlockPageElementsCount;
}
// H5EAcache.c (H5EA__cache_dblock_deserialize)
// signature
var signature = reader.ReadBytes(4);
H5Utils.ValidateSignature(signature, ExtensibleArrayDataBlock <T> .Signature);
// version
this.Version = reader.ReadByte();
// client ID
this.ClientID = (ClientID)reader.ReadByte();
// header address
this.HeaderAddress = superblock.ReadOffset(reader);
// block offset
this.BlockOffset = H5Utils.ReadUlong(reader, header.ArrayOffsetsSize);
// elements
if (this.PageCount == 0)
{
this.Elements = Enumerable
.Range(0, (int)elementCount)
.Select(i => decode(reader))
.ToArray();
}
else
{
this.Elements = new T[0];
}
// checksum
this.Checksum = reader.ReadUInt32();
}
public ExtensibleArrayDataBlock(H5BinaryReader reader, Superblock superblock, ExtensibleArrayHeader header, uint chunkSizeLength, ulong elementsCount)
{
// H5EAdblock.c (H5EA__dblock_alloc)
this.PageCount = 0UL;
if (elementsCount > header.DataBlockPageElementsCount)
{
/* Set the # of pages in the data block */
this.PageCount = elementsCount / header.DataBlockPageElementsCount;
}
// H5EAcache.c (H5EA__cache_dblock_deserialize)
// signature
var signature = reader.ReadBytes(4);
H5Utils.ValidateSignature(signature, ExtensibleArrayDataBlock.Signature);
// version
this.Version = reader.ReadByte();
// client ID
this.ClientID = (ClientID)reader.ReadByte();
// header address
this.HeaderAddress = superblock.ReadOffset(reader);
// block offset
this.BlockOffset = H5Utils.ReadUlong(reader, header.ArrayOffsetsSize);
// elements
if (this.PageCount == 0)
{
this.Elements = ArrayIndexUtils.ReadElements(reader, superblock, elementsCount, this.ClientID, chunkSizeLength);
}
// checksum
this.Checksum = reader.ReadUInt32();
}
