// 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;
}
}
}
private T?LookupElement <T>(ulong index, Func <H5BinaryReader, T> decode) where T : DataBlockElement
{
// H5EA.c (H5EA__lookup_elmt)
var chunkSizeLength = H5Utils.ComputeChunkSizeLength(this.ChunkByteSize);
/* Check if we should create the index block */
if (this.Dataset.Context.Superblock.IsUndefinedAddress(_header.IndexBlockAddress))
{
return(null);
}
/* Protect index block */
if (_indexBlock is null)
{
this.Dataset.Context.Reader.Seek((long)_header.IndexBlockAddress, SeekOrigin.Begin);
_indexBlock = new ExtensibleArrayIndexBlock <T>(
this.Dataset.Context.Reader,
this.Dataset.Context.Superblock,
_header,
decode);
}
var indexBlock = (ExtensibleArrayIndexBlock <T>)_indexBlock;
/* Check if element is in index block */
if (index < _header.IndexBlockElementsCount)
{
return(indexBlock.Elements[index]);
}
else
{
/* Get super block index where element is located */
var secondaryBlockIndex = _header.ComputeSecondaryBlockIndex(index);
/* Adjust index to offset in super block */
var elementIndex = index - (_header.IndexBlockElementsCount + _header.SecondaryBlockInfos[secondaryBlockIndex].ElementStartIndex);
/* Check for data block containing element address in the index block */
if (secondaryBlockIndex < indexBlock.SecondaryBlockDataBlockAddressCount)
{
/* Compute the data block index in index block */
var dataBlockIndex =
_header.SecondaryBlockInfos[secondaryBlockIndex].DataBlockStartIndex +
elementIndex / _header.SecondaryBlockInfos[secondaryBlockIndex].ElementsCount;
/* Check if the data block has been allocated on disk yet */
if (this.Dataset.Context.Superblock.IsUndefinedAddress(indexBlock.DataBlockAddresses[dataBlockIndex]))
{
return(null);
}
/* Protect data block */
this.Dataset.Context.Reader.Seek((long)indexBlock.DataBlockAddresses[dataBlockIndex], SeekOrigin.Begin);
var elementsCount = _header.SecondaryBlockInfos[secondaryBlockIndex].ElementsCount;
var dataBlock = new ExtensibleArrayDataBlock <T>(
this.Dataset.Context.Reader,
this.Dataset.Context.Superblock,
_header,
elementsCount,
decode);
/* Adjust index to offset in data block */
elementIndex %= _header.SecondaryBlockInfos[secondaryBlockIndex].ElementsCount;
/* Set 'thing' info to refer to the data block */
return(dataBlock.Elements[elementIndex]);
}
else
{
/* Calculate offset of super block in index block's array */
var secondaryBlockOffset = secondaryBlockIndex - indexBlock.SecondaryBlockDataBlockAddressCount;
/* Check if the super block has been allocated on disk yet */
if (this.Dataset.Context.Superblock.IsUndefinedAddress(indexBlock.SecondaryBlockAddresses[secondaryBlockOffset]))
{
return(null);
}
/* Protect super block */
this.Dataset.Context.Reader.Seek((long)indexBlock.SecondaryBlockAddresses[secondaryBlockOffset], SeekOrigin.Begin);
var secondaryBlock = new ExtensibleArraySecondaryBlock(
this.Dataset.Context.Reader,
this.Dataset.Context.Superblock,
_header,
secondaryBlockIndex);
/* Compute the data block index in super block */
var dataBlockIndex = elementIndex / secondaryBlock.ElementCount;
/* Check if the data block has been allocated on disk yet */
if (this.Dataset.Context.Superblock.IsUndefinedAddress(secondaryBlock.DataBlockAddresses[dataBlockIndex]))
{
return(null);
}
/* Adjust index to offset in data block */
elementIndex %= secondaryBlock.ElementCount;
/* Check if the data block is paged */
if (secondaryBlock.DataBlockPageCount > 0)
{
/* Compute page index */
var pageIndex = elementIndex / _header.DataBlockPageElementsCount;
/* Compute 'page init' index */
var pageInitIndex = dataBlockIndex * secondaryBlock.DataBlockPageCount + pageIndex;
/* Adjust index to offset in data block page */
elementIndex %= _header.DataBlockPageElementsCount;
/* Compute data block page address */
var dataBlockPrefixSize =
// H5EA_METADATA_PREFIX_SIZE
4UL + 1UL + 1UL + 4UL +
// H5EA_DBLOCK_PREFIX_SIZE
this.Dataset.Context.Superblock.OffsetsSize + _header.ArrayOffsetsSize +
// H5EA_DBLOCK_SIZE
secondaryBlock.ElementCount * _header.ElementSize + /* Elements in data block */
secondaryBlock.DataBlockPageCount * 4; /* Checksum for each page */
var dataBlockPageAddress = secondaryBlock.DataBlockAddresses[dataBlockIndex] + dataBlockPrefixSize +
(pageIndex * secondaryBlock.DataBlockPageSize);
/* Check if page has been initialized yet */
var pageBitmapEntry = secondaryBlock.PageBitmap[pageIndex / 8];
var bitMaskIndex = (int)pageIndex % 8;
if ((pageBitmapEntry & H5Utils.SequentialBitMask[bitMaskIndex]) == 0)
{
return(null);
}
/* Protect data block page */
this.Dataset.Context.Reader.Seek((long)dataBlockPageAddress, SeekOrigin.Begin);
var dataBlockPage = new DataBlockPage <T>(
this.Dataset.Context.Reader,
_header.DataBlockPageElementsCount,
decode);
/* Set 'thing' info to refer to the data block page */
return(dataBlockPage.Elements[elementIndex]);
}
else
{
/* Protect data block */
this.Dataset.Context.Reader.Seek((long)secondaryBlock.DataBlockAddresses[dataBlockIndex], SeekOrigin.Begin);
var dataBlock = new ExtensibleArrayDataBlock <T>(
this.Dataset.Context.Reader,
this.Dataset.Context.Superblock,
_header,
secondaryBlock.ElementCount,
decode);
/* Set 'thing' info to refer to the data block */
return(dataBlock.Elements[elementIndex]);
}
}
}
}