4 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	12efbc1beb	rugnux: emit non-standard mmCIF items under a "jfjoch" reserved prefix, not pdbx_ ... ISa and the twinning indicators (L-test means, second moment of I) have no standard mmCIF item. They were written as _reflns.pdbx_* names, borrowing the wwPDB PDBx/mmCIF dictionary's reserved prefix and so masquerading as standard items the dictionary does not actually define. Move them to the IUCr-sanctioned local-data-name extension: a private reserved prefix on the attribute of the existing _reflns category (_reflns.jfjoch_*), matching the DDL2 pattern the spec gives for private items. Write-only tags with no reader, so this is a self-contained, back-compatible rename. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-10 13:01:05 +02:00
leonarski_fandClaude Opus 4.8	a4cc908ff1	rugnux: run the L-test on rhombohedral data + write twinning stats to CIF ... The Padilla-Yeates L-test paired each reflection with a neighbour two steps along an axis ((h+2,k,l) etc.). A step of 2 preserves the reflection condition of P/I/C/F/A/B lattices but violates R-centring (-h+k+l = 0 mod 3, since 2 != 0 mod 3), so every neighbour was systematically absent -> zero pairs, and the L-test silently did not run on ANY rhombohedral crystal (twinning there was left to the weaker second-moment test alone). Add diagonal (1,1,0)/(1,1,3) fallback steps that preserve the mod-3 condition in both obverse and reverse settings, tried only when the axis steps find no present partner (P/I/C/F behaviour unchanged). On the twinned R3 insulin the L-test now runs: 25k pairs, <L^2> = 0.224 -> twinning detected. Also write the twinning indicators to the output mmCIF next to ISa: _reflns.pdbx_L_test_mean_abs_L / _L_test_mean_L_squared / _second_moment_I, as free-text pdbx values, guarded on pair/reflection count. Threaded the TwinningAnalysisResult into WriteReflections (both the full-pipeline and --scale callers). Note: on rhombohedral lattices the L-test reads ~0.03 lower than on P/I/C/F (its allowed step is slightly more local), so it separates the insulin twin pair only weakly (twinned 0.398 vs untwinned 0.427) and the second moment remains the cleaner discriminator there. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-09 21:59:37 +02:00
leonarski_f	d6389e12da	v1.0.0-rc.156 (#66) ... 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>	2026-07-03 19:18:56 +02:00
leonarski_f	fc68a9baed	v1.0.0-rc.146 (#56) ... 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_process: Generate a dedicated file (_process.h5), which can be used as a replacement for the _master.h5 file for a reanalyzed dataset. jfjoch_process: Improve the performance of scaling and merging, implement on the fly scaling. jfjoch_writer: All final data analysis results are repopulated in the _master.h5 file. jfjoch_scale: Dedicated tool for rescaling/merging existing data. jfjoch_viewer: Fix bugs where pixel labels where displayed on a wrong pixel. WARNING! Scaling and merging are experimental at the moment, and may not provide reasonable results for the time being. Reviewed-on: #56	2026-05-28 18:48:35 +02:00