bitshuffle_hperf is an x86-only implementation - its entire vector body sits behind
__i386__/__x86_64__, so on aarch64 every entry point compiles down to the scalar
fallback. Measured against its own SIMD path that costs 8.3x on encode and 3.8x on
decode, and it is the transform behind every compressed image the writer produces and
every one the reader, preview and XDS plugin take apart again.
The classic bitshuffle vendored beside it does have an aarch64 NEON path, and is already
compiled into the same target, so this costs nothing new. BitShuffleBlock.h picks
bshuf_trans_bit_elem/bshuf_untrans_bit_elem there and keeps bitshuf_encode_block /
bitshuf_decode_block everywhere else, where hperf is about twice classic SSE2 and remains
the better choice. The expected aarch64 gain is ~2.5x encode / ~1.7x decode: classic NEON
is 128-bit and carries an extra pass, so it recovers part of the gap rather than all of
it. The condition mirrors USEARMNEON in bitshuffle_core.c exactly, because with NEON off
the classic scalar path is slower than hperf's and must not be selected.
Swapping implementations is only safe while the two agree bit for bit - otherwise an ARM
build would write files an x86 build could not read. They do: verified byte-identical
output and mutual cross-decoding for elem_size 1/2/4/8 over block sizes from 8 to 65536
elements. Both are always compiled in, so the new test holds them to it on every
architecture, not just the one that would notice.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
JFJochDecompressHperfPtr took source_size and never looked at it: every
per-block length was read out of the stream and passed straight to
LZ4_decompress_safe/ZSTD_decompress as the source length, with src_ptr
advanced by it. The only check happened after the whole buffer had
already been walked. A truncated frame, or a block header claiming
0x7fffffff, read far past the end of a heap buffer - reachable from the
ZeroMQ CBOR path and from any HDF5 chunk the XDS plugin is handed.
block_size == 0 satisfied the "% BSHUF_BLOCKED_MULT" test and then
divided at nelements / block_size, and source_size < 12 underflowed
source_size - 12 to about 2^64. Both are now rejected.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use.
* jfjoch_process: Major rotation (rot3d) data processing overhaul - robust profile-fit integration, Cauchy-loss scaling with optional absorption surface, de-novo indexing and space-group/centering determination fixes, and merging statistics + ISa in the mmCIF output.
* jfjoch_process: Add EXPERIMENTAL ice-ring detection (--detect-ice-rings) that excludes ice reflections from scaling.
* Compression: Add BSHUF_ZSTD_RLE_HUFF, make compression size-aware (drop frames that don't fit rather than aborting), and add the jfjoch_recompress tool.
* jfjoch_viewer: Report "Multiple lattices detected" and grey out "Analyze dataset" on a live connection.
* jfjoch_broker: Write smargon chi/phi goniometer positions to NXmx; read sensor thickness/material from HDF5 metadata.
* CI: Build Windows (CUDA and non-CUDA) installers.Reviewed-on: #66
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use.
* jfjoch_broker: Add EXPERIMENTAL pixelrefine mode for image processing
* jfjoch_broker: Allow to load user mask from 8-bit and 16-bit TIFF files
* jfjoch_broker: Add ROI calculation in non-FPGA workflow
* jfjoch_broker: Fixes to TCP image pusher
* jfjoch_broker: Remove NUMA bindings
* jfjoch_broker: Improvements to indexing
* jfjoch_broker: For PSI EIGER, trimming energies are taken from the detector configuration (now compulsory) instead of hardcoded values
* jfjoch_writer: Save ROI definitions and the per-pixel ROI bitmap in the master file; azimuthal ROIs support phi (angular) sectors
* jfjoch_viewer: Major redesign with dockable panels and saved layouts, plus on-canvas creation/move/resize of box, circle and azimuthal ROIs
* jfjoch_viewer: Run jfjoch_process reprocessing jobs from inside the GUI and overlay per-run results
Reviewed-on: #63
This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144.
* jfjoch_broker: Improve azimuthal integration (add <I^2> calculation)
* jfjoch_broker: Fixes around indexing, aiming to handle multi-lattice crystals (work in progress, it is not fully integrated)
* jfjoch_writer: Save mean(I), stddev(I), and count(I) for each azimuthal bin
Reviewed-on: #58
This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132.
* Multiple small bug fixes scattered across the whole code base. (detected with GPT-5.4)
* jfjoch_viewer: Improve image render performance
Reviewed-on: #44
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132.
* jfjoch_broker: Add better locking for detector object - should help, when detector initialization takes too long
* jfjoch_writer: Enable writing single, integrated HDF5 file with both data and metadata
* XDS plugin: Add generation of Jungfraujoch plugin for XDS
* CI: Add tests with XDS and DIALS (`xia2.ssx`)
Reviewed-on: #43
leonarski_fandClaude Opus 5