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Jungfraujoch/tools
leonarski_fandClaude Opus 4.8 f261adf42a
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tools: add jfjoch_recompress (bitshuffle/LZ4 -> bitshuffle/zstd)
New offline tool that re-compresses /entry/data/data of a _data_NNNNNN.h5 file
from bitshuffle/LZ4 to the standard bitshuffle/Zstd HDF5 filter. Every other
object (groups, datasets, attributes, the dataset's own attributes,
dims/dtype/chunking/block size) is reproduced unchanged.

It writes a fresh file - only /entry/data/data is re-encoded, every other object
is H5Ocopy'd verbatim - which then atomically replaces the original via rename().
This needs no h5repack (the new file has no leftover space) and is crash-safe
(the original is opened read-only until the rename). Frames are streamed one at a
time through the registered bitshuffle filter (decompress LZ4, compress Zstd), so
it is dtype-agnostic and never holds the whole dataset in memory.

Output is read by the standard bitshuffle+zstd HDF5 plugin (verified against the
hdf5plugin/DIALS libh5bshuf.so, which links libzstd and supports the zstd mode).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
2026-06-27 15:24:30 +02:00
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