protected override ChunkInfo GetChunkInfo(ulong[] chunkIndices)
{
if (this.Dataset.InternalFilterPipeline is null)
{
if (_btree2_no_filter is null)
{
this.Dataset.Context.Reader.Seek((long)this.Dataset.InternalDataLayout.Address, SeekOrigin.Begin);
Func <BTree2Record10> decodeKey
= () => this.DecodeRecord10(this.ChunkRank);
_btree2_no_filter = new BTree2Header <BTree2Record10>(this.Dataset.Context.Reader, this.Dataset.Context.Superblock, decodeKey);
}
// get record
var success = _btree2_no_filter.TryFindRecord(out var record, record =>
{
// H5Dbtree2.c (H5D__bt2_compare)
return(H5Utils.VectorCompare(this.ChunkRank, chunkIndices, record.ScaledOffsets));
});
return(success
? new ChunkInfo(record.Address, this.ChunkByteSize, 0)
: ChunkInfo.None);
}
else
{
if (_btree2_filter is null)
{
this.Dataset.Context.Reader.Seek((long)this.Dataset.InternalDataLayout.Address, SeekOrigin.Begin);
var chunkSizeLength = H5Utils.ComputeChunkSizeLength(this.ChunkByteSize);
Func <BTree2Record11> decodeKey =
() => this.DecodeRecord11(this.ChunkRank, chunkSizeLength);
_btree2_filter = new BTree2Header <BTree2Record11>(this.Dataset.Context.Reader, this.Dataset.Context.Superblock, decodeKey);
}
// get record
var success = _btree2_filter.TryFindRecord(out var record, record =>
{
// H5Dbtree2.c (H5D__bt2_compare)
return(H5Utils.VectorCompare(this.ChunkRank, chunkIndices, record.ScaledOffsets));
});
return(success
? new ChunkInfo(record.Address, record.ChunkSize, record.FilterMask)
: ChunkInfo.None);
}
}
protected override ChunkInfo GetChunkInfo(ulong[] chunkIndices)
{
// H5Dfarray.c (H5D__farray_idx_get_addr)
/* Calculate the index of this chunk */
var chunkIndex = chunkIndices.ToLinearIndexPrecomputed(this.DownMaxChunkCounts);
/* Check for filters on chunks */
if (this.Dataset.InternalFilterPipeline is not null)
{
var chunkSizeLength = H5Utils.ComputeChunkSizeLength(this.ChunkByteSize);
var element = this.GetElement(chunkIndex, reader =>
{
return(new FilteredDataBlockElement()
{
Address = this.Dataset.Context.Superblock.ReadOffset(reader),
ChunkSize = (uint)H5Utils.ReadUlong(reader, chunkSizeLength),
FilterMask = reader.ReadUInt32()
});
});
return(element is not null
? new ChunkInfo(element.Address, element.ChunkSize, element.FilterMask)
: ChunkInfo.None);
}
else
{
var element = this.GetElement(chunkIndex, reader =>
{
return(new DataBlockElement()
{
Address = this.Dataset.Context.Superblock.ReadOffset(reader)
});
});
return(element is not null
? new ChunkInfo(element.Address, this.ChunkByteSize, 0)
: ChunkInfo.None);
}
}
protected override ChunkInfo GetChunkInfo(ulong[] chunkIndices)
{
// H5Dearray.c (H5D__earray_idx_get_addr)
/* Check for unlimited dim. not being the slowest-changing dim. */
ulong chunkIndex;
if (_unlimitedDim > 0)
{
var swizzledCoords = new ulong[this.ChunkRank];
/* Compute coordinate offset from scaled offset */
for (int i = 0; i < this.ChunkRank; i++)
{
swizzledCoords[i] = chunkIndices[i] * this.ChunkDims[i];
}
H5Utils.SwizzleCoords(swizzledCoords, _unlimitedDim);
/* Calculate the index of this chunk */
var swizzledScaledDims = swizzledCoords
.Select((swizzledCoord, i) => H5Utils.CeilDiv(swizzledCoord, _swizzledChunkDims[i]))
.ToArray();
chunkIndex = swizzledScaledDims.ToLinearIndexPrecomputed(_swizzledDownMaxChunkCounts);
}
else
{
/* Calculate the index of this chunk */
chunkIndex = chunkIndices.ToLinearIndexPrecomputed(this.DownMaxChunkCounts);
}
/* Check for filters on chunks */
if (this.Dataset.InternalFilterPipeline is not null)
{
var chunkSizeLength = H5Utils.ComputeChunkSizeLength(this.ChunkByteSize);
var element = this.GetElement(chunkIndex, reader =>
{
return(new FilteredDataBlockElement()
{
Address = this.Dataset.Context.Superblock.ReadOffset(reader),
ChunkSize = (uint)H5Utils.ReadUlong(reader, chunkSizeLength),
FilterMask = reader.ReadUInt32()
});
});
return(element is not null
? new ChunkInfo(element.Address, element.ChunkSize, element.FilterMask)
: ChunkInfo.None);
}
else
{
var element = this.GetElement(chunkIndex, reader =>
{
return(new DataBlockElement()
{
Address = this.Dataset.Context.Superblock.ReadOffset(reader)
});
});
return(element is not null
? new ChunkInfo(element.Address, this.ChunkByteSize, 0)
: ChunkInfo.None);
}
}
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]);
}
}
}
}