16 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	545ebdf868	Merge: per-crystal CC1/2-delta rejection (--reject-delta-cchalf) ... CrystFEL deltaCChalf-style per-crystal quality filter for heterogeneous serial data. Each image is assigned to one CC1/2 half, so removing it perturbs only that half's per-reflection means; deltaCChalf_i = CC1/2(all) - CC1/2(without image i). A negative value means dropping the image RAISES CC1/2 (it disagrees with the consensus). Images whose deltaCChalf is a low-side statistical outlier (< mean - N*stddev) are skipped when merging. Reference-free. Two passes over the retained integration outcomes; per-image contributions are re-derived rather than stored, so memory stays O(unique reflections + images) for full 200k-frame runs. New CLI flag --reject-delta-cchalf <N> (default: off). Validation (jet FFBIDX +C+S, sigma4): removing 17/4000 (3 sigma) raises CC1/2 95.1->96.1%, CCref 54.9->55.2; 2 sigma -> 96.1/55.3. Dataset-appropriate: it HELPS heterogeneous serial data (some crystals genuinely bad) but slightly trims a homogeneous single rotation crystal (c2 94.6->93.8 - no bad crystals, the relative cut still removes the tail), so it is opt-in. R-free is the real test (user's full 200k). Note: the reported overall N_obs still counts all observations; the exported merge (and CC1/2) correctly exclude the rejected images. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-16 12:32:52 +02:00
leonarski_fandClaude Opus 4.8	6f733d74c2	Merge: make outlier rejection a ScalingSettings parameter + CLI flag, default 6 ... Promote the per-observation merge outlier rejection from the temporary PR_REJECT env knob to a real setting: ScalingSettings::OutlierRejectNsigma (default 6, <=0 disables), driven into MergeOnTheFly via the constructor, with a --reject-outliers CLI flag in jfjoch_process. Default-on at 6 sigma matches XDS (MISFITS/REJECT) and DIALS (normalised-deviation test); it validated on the full-jet R-free (0.2625 -> 0.2585). Applies to both the PixelRefine and classical merge paths. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-15 12:42:25 +02:00
leonarski_fandClaude Opus 4.8	a47b376dc3	Merge: per-observation outlier rejection (env-gated PR_REJECT) ... At the jet's ~1000x multiplicity R-free is bias-limited, and the merge had NO outlier rejection - serial data zingers/overlaps/mis-indexed frames bias every merged mean. Add a robust per-observation cut: drop observations whose corrected intensity lies > reject_nsigma error-model sigmas from the reflection's MEDIAN. The error-model sigma already captures the genuine (partiality) scatter, and the median is a robust centre, so only the tail beyond the real spread is removed - not good partials. The median is computed in RefineErrorModel (which already pools the observations per reflection); AddImage applies the cut. Env-gated via PR_REJECT=<nsigma> (off by default); logs the count removed. On the jet (CC proxy) it lifts CCref +8 (nsigma 6, 0.6% cut) to +11 (nsigma 3, 7.4% cut) - the cut is vs the data's own median, not the reference, so the gain is real cleaner means. R-free validation + the nsigma sweet spot (over-rejection risk at low nsigma) are for Filip's full-jet R-free. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-14 20:56:53 +02:00
leonarski_fandClaude Opus 4.8	c93d381dc8	Error model: harden the fit against pathological inputs (code review) ... Addresses code-review findings on RefineErrorModel: - Floor the 1/dev^2 bin weight relative to the data scale (1e-3 of the median bin dev^2), not an absolute 1e-30: a near-zero-scatter bin could otherwise acquire a runaway weight and hijack the global (a,b) fit. - Reject a near-collinear normal-equation system relatively (det > 1e-10*Ass*AII) instead of with an absolute threshold that an ill-conditioned fit can pass. - Reset the model to identity at entry so any early return leaves it inactive rather than keeping a stale a/b alongside a freshly-cleared mean map (which would make CorrectedSigma fall back to the per-observation I). - PixelRefine: correct the orient_prior comment - with the sweep on, the LSQ anchor is the swept orientation (intended), not the spot-centroid one. Verified unchanged on the lyso test set (ISa 1.1, CC1/2 90.3%). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-12 18:53:02 +02:00
leonarski_fandClaude Opus 4.8	e6a50b45c7	Integration: mean background + global error model (trustworthy sigmas) ... Background estimate: use the mean of the local ring, not the median. For a right-skewed (Poisson) background the median sits below the mean, so subtracting it under-subtracts and biases every weak intensity positive; over multiplicity this becomes fake <I/sig> of a few in no-signal high-resolution shells. Fixed in both PixelRefine and BraggIntegrate2D (the classical route had the same bug). <I/sig> now tracks CC honestly and the true resolution limit is visible. Error model: fit a global a, b (XDS form sigma'^2 = a*sigma^2 + (b*I)^2) from the scatter of symmetry equivalents at the merge level (so both integrators benefit), and print it with ISa = 1/b in jfjoch_process. The (b*I)^2 term uses the reflection mean (not the per-observation I_i, which biases the weights and collapses CC); a,b come from a relative-weighted bin regression. Replaces the earlier per-resolution-shell variant, which was partly masking the background bias. METHODS.md: document both (Sections 6-7), integrator-agnostic. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-12 18:39:32 +02:00
leonarski_f	e051eed033	jfjoch_process: Remove postrefinement	2026-06-09 19:46:39 +02:00
leonarski_f	5735302691	Merge: CC1/2 limit adjustment	2026-06-09 11:06:16 +02:00
leonarski_f	32e91f7287	Minor fixes	2026-06-08 15:56:20 +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_fandtakaba_k	230480e390	v1.0.0-rc.138 (#48) ... 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: Cleanup DECTRIS start-up code to enable a shorter start time jfjoch_broker: Allow for asynchronous start to allow overlapping detector configuration with other beamline preparations jfjoch_broker: Goniometer axis name is converted to lowercase jfjoch_broker: Fix bug, where wrong HTTP error codes were returned jfjoch_broker: Improve sigma estimation during merging (K. Takaba) --------- Co-authored-by: takaba_k <kiyofumi.takaba@psi.ch> Reviewed-on: #48 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-27 19:56:14 +02:00
leonarski_f	166fcdb68f	v1.0.0-rc.131 (#39) ... 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: Fix bug in saving JUNGFRAU calibration (pedestal/pedestalRMS) * jfjoch_viewer: Fix calibration (pedestal) images being open flipped * jfjoch_process: Add space group detection (EXPERIMENTAL) Reviewed-on: #39	2026-03-07 11:34:04 +01:00
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	3036b1d37f	v1.0.0-rc.128 (#35) ... 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: Handle properly reuse of image buffer locations * jfjoch_broker: Fix bug in counting idle slots * jfjoch_broker: Force obtuse angle for monoclinic cells * jfjoch_process: Change scaling refinement tolerance Reviewed-on: #35 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-03-03 22:24:44 +01:00
leonarski_f	f3e0a15d26	v1.0.0-rc.127 (#34) ... 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: Default EIGER readout time is 20 microseconds * jfjoch_broker: Multiple improvements regarding performance * jfjoch_broker: Image buffer allows to track frames in preparation and sending * jfjoch_broker: Dedicated thread for ZeroMQ transmission to better utilize the image buffer * jfjoch_broker: Experimental implementation of transmission with raw TCP/IP sockets * jfjoch_writer: Fixes regarding properly closing files in long data collections * jfjoch_process: Scale & merge has been significantly improved, but it is not yet integrated into mainstream code Reviewed-on: #34	2026-03-02 15:57:12 +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