6 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	f0799f780b	rugnux: drop edge-of-sweep truncated fulls + honest R-meas over accepted obs ... From a fresh decomposition of the low-resolution-shell R-meas gap vs XDS on the reference lysozyme rotation crystal (7.6% vs 2.9%), two rot3d scale/merge changes: - New --min-captured-fraction (default 0.5 for rotation, off otherwise): drop a combined full whose rocking curve was captured below this fraction. These edge-of-sweep, partiality-extrapolated fulls (sweep start/end) are biased and inflate the low-res R-meas. Dropping them lowers low-shell R-meas 7.6->5.5% and *improves* external accuracy (CC vs the F-model and vs an independent dataset, and the ANODE anomalous S-peak 0.93->0.94x XDS) - unlike --min-partiality, which lowers R-meas cosmetically while degrading accuracy. Threaded through ScalingSettings and both the GPU and CPU combine. - R-meas reporting fix: the R_meas re-walk counted observations the merge had rejected as outliers (XDS excludes its misfits before its R-factor). The accumulate pass now flags each rejected full and the R_meas pass skips it, in both the GPU and CPU paths. Merged intensities / ISa / CC1/2 unchanged (verified byte-identical external accuracy); low-shell R-meas 7.6->6.5%. No-op when --reject-outliers 0. Combined default rotation low-shell R-meas 7.6->5.1%, ISa 17.2->17.5, external accuracy equal-or-better than baseline and XDS. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-10 20:13:06 +02:00
leonarski_fandClaude Opus 4.8	4f3153d6c7	rugnux: automatic CC1/2-logistic high-resolution cutoff ... Merge/report/write to the CC1/2 fall-off instead of the detector edge. After the final merge, fit a logistic to a fine-binned CC1/2 profile and cut one shell past cc_target (default 0.30) - generous, DIALS-style. Only the written MTZ/CIF and the reported shell table are trimmed; scaling, the 3D combine and the error model still run over the full range, and the per-image _process.h5 keeps full data for re-scaling. The de-novo P1 merge that feeds the space-group search is never cut (gated on the final merge). - ScalingSettings: resolution_cutoff {Off,CCHalfLogistic}, resolution_cc_target, report_shell_count (report shell count is now configurable). - New ResolutionCutoff.{h,cpp}: ComputeCCHalfLogisticCutoff (fine-bin CC1/2 + grid/refine logistic fit + one-shell extension + degeneracy/low-res guards). - Wired into RotationScaleMerge (rotation) and MergeOnTheFly/Rugnux (stills), plus the rugnux --scale path. - CLI: --resolution-cutoff cc-logistic|off, --resolution-cc-target, --resolution-shells. --scaling-high-resolution stays the manual override (wins and disables the auto-cut). Validated on the 24-crystal battery: no crashes (incl. Benas/cytC_10/Thau_9); --resolution-cutoff off is bit-identical to baseline; cutoffs reproduce the design table within ~0.05 A (lysoC 1.30, Ins_I 1.43, cytC_2 1.68, EcwtCQ244-E3 1.54); good-to-edge datasets (lyso_ref, EP_cs_02-10) correctly keep the full range. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-09 17:34:49 +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	54c667190f	v1.0.0-rc.155 (#65) ... 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: Remove pixelrefine option (replaced with ProfileIntegrate2D) * jfjoch_viewer: Some graphical improvements. * jfjoch_viewer: Simplify und unify data analysis settings. * jfjoch_writer: Add TCP keepalive to increase robustness if jfjoch_broker "dies" in the middle of data acquisition. Reviewed-on: #65	2026-06-25 22:01:48 +02:00
leonarski_f	75e401f0e5	v1.0.0-rc.153 (#63) ... 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	2026-06-23 20:29:49 +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