6 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	f60768d49c	Bragg integration: drop the 2% sigma floor and carry the background variance ... Two changes to the same variance chain; they are in one commit because the second exists to remove an assumption the first was breaking, and separating them leaves a tree that is correct only by luck. The reported sigma was floored at 2% of the intensity, a per-partial I/sigma cap of 50. It applied only to the box-sum seed, never to the profile fit, so the shipped default was unaffected - but the combine back-derives each partial's non-signal variance as sigma^2 - I, and a floored sigma makes that quantity mean nothing. It then read corr^2 * (0.0004 I^2 - I), which is not a background variance. Measured on --integrator boxsum: the reported sigma understated the true scatter by up to 16x at I ~ 21000 counts per partial, and pooled_I amplified a 1 ct/px background drift into an 11.5% intensity error on the strongest reflections. What the floor stood in for - that at high intensity the error is systematic rather than counting - is already carried downstream, twice: the fitted b in v = a*sigma^2 + (b*I)^2, measured from the data rather than assumed, and SigmaWithSystematicFloor on the merged sigma. The floor was that idea applied one level too early with a hardcoded b of 0.02. It arrived without a test or a setter and was unreachable from the CLI, the API and the config. The merge now takes the non-signal variance the integrator actually measured instead of inverting sigma^2 = I + N. That identity is exact for a box sum once the floor is gone and was never exact for a profile fit, whose sigma^2 = 1/den + (wsum/den)^2 * bkg_var is formed against a fitted intensity. The value is carried through BraggFitResult, Reflection and Obs, both engines, both merges, and the process-file round trip; files written before this change are read with the term absent, which is what they had. Battery, 37 crystals, paired: space groups unchanged, reflection sets unchanged, median delta zero on R_meas and CC1/2. --integrator boxsum on the reference crystal goes ISa 8.9 -> 20.2 with a 0.947 -> 1.032. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-09 19:10:57 +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
leonarski_f	64002f1e29	v1.0.0-rc.129 (#36) ... 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.124. * jfjoch_broker: Significant improvements in TCP image socket, as a viable alternative for ZeroMQ sockets (only a single port on broker side, dynamically change number of writers, acknowledgments for written files) * jfjoch_broker: Delta phi is calculated also for still data in Bragg prediction * jfjoch_broker: Image pusher statistics are accessible via the REST interface * jfjoch_writer: Supports TCP image socket and for these auto-forking option Reviewed-on: #36 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-03-05 22:13:12 +01:00
leonarski_f	1ab257af6c	v1.0.0-rc.125 (#32) ... This is an UNSTABLE release. This version adds scalign and merging. These are experimental at the moment, and should not be used for production analysis. If things go wrong with analysis, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Improve logic on switching on/off spot finding * jfjoch_broker: Increase maximum spot count for FFBIDX to 65536 * jfjoch_broker: Increase default maximum unit cell for FFT to 500 A (could have performance impact, TBD) * jfjoch_process: Add scalign and merging functionality - program is experimental at the moment and should not be used for production analysis * jfjoch_viewer: Display partiality and reciprocal Lorentz-polarization correction for each reflection * jfjoch_writer: Save more information about each reflection Reviewed-on: #32 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-02-18 16:17:21 +01:00
leonarski_f	07fe4dd3bb	v1.0.0-rc.124 (#31) ... This is an UNSTABLE release. This version significantly rewrites code to predict reflection position and integrate them, especially in case of rotation crystallography. If things go wrong with analysis, it is better to revert to 1.0.0-rc.123. * jfjoch_broker: Improve refection position prediction and Bragg integration code. * jfjoch_broker: Align with XDS way of calculating Lorentz correction and general notation. * jfjoch_writer: Fix saving mosaicity properly in HDF5 file. * jfjoch_viewer: Introduce high-dynamic range mode for images * jfjoch_viewer: Ctrl+mouse wheel has exponential change in foreground (+/-15%) * jfjoch_viewer: Zoom-in numbers have better readability Reviewed-on: #31 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-02-01 13:29:33 +01:00
leonarski_f	c67337cfe1	v1.0.0-rc.72	2025-09-08 20:28:59 +02:00