32 Commits

Author	SHA1	Message	Date
leonarski_f	e1e2ca8e49	IndexAndRefine: unify cell setting across indexers, keep FFBIDX neutral ... Follow-up to 40da1aab. Conventionalise the indexed lattice for BOTH indexers when cell+SG are given, so every frame reports its cell in ONE consistent setting per space group (mixed axis orders like [78,78,38] vs [38,78,78] index the same reflection as different HKLs and cannot be merged). Use LatticeSearch's conventional cell when its detected symmetry agrees with the user's space group. On noisy frames LatticeSearch can pick an alternative Bravais setting (e.g. the sqrt2 C-centred description of a primitive tetragonal cell, [78,78,38]->[110,111,38]) whose system disagrees; there: - FFBIDX already returns the reference setting (c-last), consistent with the conventional frames, so its raw lattice is safe -> use it. This recovers the ~3% of frames the unconditional version lost: FFBIDX is byte-for-byte neutral. - de-novo (FFT/FFTW) return a Niggli-primitive cell with a DIFFERENT axis order (c-first); merging it with the conventional (c-last) frames would corrupt the data -> reject the frame instead. Validation (lyso): FFBIDX c2 71.44% / jet 27.15% (both unchanged vs raw-lattice baseline, CC1/2 94.6 / 91.9); FFT c2 +C+S 92.72% (CC1/2 95.8, all c-last, consistent); FFT c2 de-novo 95.44% (unchanged). Verified per-frame that the c-axis (~38A) is axis 2 in every merged frame - no axis-order mixing. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-15 22:50:56 +02:00
leonarski_f	40da1aab13	IndexAndRefine: conventionalise de-novo lattice when cell+SG are given ... Providing both a unit cell (-C) and space group (-S) silently broke the de-novo indexers (FFT/FFTW) -> 0% indexing, while each flag alone worked. Root cause: the `sg && GetUnitCell()` branch fed the indexer's raw lattice straight into symmetry-constrained refinement. FFBIDX returns the lattice already in the reference setting, but FFT/FFTW return an arbitrarily-oriented Niggli-primitive cell; enforcing the crystal system on its mis-assigned axes rejects every frame. Fix: for de-novo indexers only, reduce the lattice to the conventional setting (LatticeSearch) before refinement. FFBIDX keeps using its raw lattice as-is, so it is byte-identical to before (no regression). niggli_class stays unassigned (0) in this branch - it is a property of the primitive cell incl. centering, which LatticeSearch cannot recover from a user-supplied (possibly centered, e.g. C2) cell. A proper primitive-cell indexing path (CrystFEL-style) is deferred. Validation (lyso, -C79,79,38 -S96): crystal 2 FFT : 0% -> 94.9% (CC1/2 95.8, CCref 92.7) = de-novo quality crystal 2 FFBIDX: 71.4% (CC1/2 94.6) - byte-identical jet FFBIDX: 27.2% (CC1/2 91.9) - byte-identical (Jet FFT stays 0% - that is a separate, still-open issue: de-novo finds no consensus on the weak serial-still frames, 0% even without -S; to investigate.) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-15 20:35:03 +02:00
leonarski_f	ecdb7048a0	PixelRefine: drop crystal-system idealisation, use the indexed cell as-is ... PixelRefine no longer refines the cell, so the symmetry-constrained cell parameterisation inherited from XtalOptimizer has no manifold to constrain. The decompose->rebuild round-trip (Gram-Schmidt orientation + symmetry B matrix) merely reconstructed the lattice columns it started from, and for non-triclinic systems it re-idealised the indexed cell (averaging a,b for tetragonal; a,b,c for cubic; forcing alpha=gamma=90). Replace both six-way switches (PredictedNode and BuildParameterBlocks) with a single path: take the three real-space lattice columns (latt.Vec0/1/2()) directly and form the reciprocal node via the general cross-product inverse. This reproduces every crystal system exactly from the actual cell, is more faithful (no re-idealisation), and removes the crystal_system field plus two now-unused includes. PredictedNode de-templated (only ever called with double). Crystal symmetry still lives where it belongs: indexing (upstream) and merging (downstream via the space-group HKL key). A/B (both lyso P4_3 2_1 2 crystals, refined under tetragonal constraint, so the old idealisation was already a no-op): stat tables bit-identical across all shells -- crystal 2 CC1/2 94.6% / CCref 92.5%, jet CC1/2 91.9% / CCref 55.8% -- the only delta is 4th-digit float-ordering noise in the error-model b coefficient (0.8143->0.8141, same ISa). Same merged intensities => R-free unchanged. Net -81 lines. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-15 14:11:26 +02:00
leonarski_f	8a9d80eb71	PixelRefine: profile multiplier as --profile-multiplier flag; outlier rejection default off ... (1) Promote the Term-2 profile-width multiplier from the PR_RMULT env knob to a real BraggIntegrationSettings::profile_multiplier (default 6) + jfjoch_process --profile-multiplier flag. Removes the last PR_* env knob; IndexAndRefine reads the setting. (2) Flip the merge outlier rejection default to OFF (ScalingSettings outlier_reject_nsigma 6 -> 0); it stays available via --reject-outliers <nsigma>, since it helps the jet R-free but is dataset-dependent (drops crystal-2 CCref). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-15 13:48:11 +02:00
leonarski_f	102a2a7c81	PixelRefine: strip experimental env knobs (orientation, sweep, Lorentz, ML census) ... Remove the env-gated experiments that A/B'd to dead-ends or are no longer needed, returning PixelRefine to the clean factored Terms 1+2 plus the one validated keeper (r1_multiplier, default 6): - PR_ORIENT (per-image orientation refinement): R-free no-op (0.2618 vs 0.2625) - XtalOptimizer's orientation is already optimal. Removes ShoeboxResidual, OrientationRegularizer, PixelObs::weight, the refinement block and its fields. - PR_SWEEP (orientation + cell-scale sweep): R-free no-op, degraded high-res CC1/2 (per-image overfit). Removes SweepOrientationCell and its fields. - PR_LORENTZ (rotation Lorentz/zeta): hurt both directions (the factored partiality already subsumes it); was already reverted. - PR_MLCENSUS (multi-lattice census in AnalyzeIndexing): served its purpose (~3-5% of jet frames are multi-lattice; shelved). PR_RMULT (the validated Term-2 multiplier knob) is kept. Defaults unchanged: crystal 2 / jet / hybrid -R -r pixelrefine all reproduce. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-15 13:34:54 +02:00
leonarski_f	45ee8c2b40	PixelRefine: env-gated orientation + cell-scale sweep (PR_SWEEP) for R-free A/B ... R-free validation (full jet, 1.5 A) confirmed the r1_multiplier fix: PR x6 beats traditional (R-free 0.2625 vs 0.2802), the multiplier optimum is ~6 (x6==x9 on R-free; x9 only buys CC1/2 internal consistency), and per-image orientation *refinement* is a no-op (0.2618 vs 0.2625). Re-adds the reference-driven orientation + uniform cell-scale SWEEP behind PR_SWEEP (off by default) to test whether the cell-scale degree of freedom - which the gradient orientation refinement lacks, and which moves the high-res shells radially - helps R-free at 1.5 A on serial data. CCref is a near-no-op on the jet (as for the gradient path), but that does not certify R-free, so it is left for validation. NOTE: PR_RMULT / PR_ORIENT / PR_SWEEP remain temporary diagnostic env knobs; once the sweep R-free is in, bake r1_multiplier=6, drop the no-op paths, strip the knobs. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-14 19:59:50 +02:00
leonarski_f	cfcd4c9e56	PixelRefine: R1 multiplier (fix tight-Term2 regression) + env-gated orientation refine ... Full-jet R-free showed the factored model regressed vs the traditional pipeline (R-free 0.34 vs 0.26, CCref 58 vs 76), traced to Term 2 using the raw measured profile width: it is too tight (~0.002 A^-1), so the template sits off the ~0.4 px centroid-floor scatter and underestimates the intensity (box-sum is immune). Fix, XDS-style (integrate over ~6 sigma): multiply the measured R1 by r1_multiplier (default 6) before use. On the jet at 1.3 A this recovers CCref 55.2 -> 59.3 (~ traditional's 60.5); crystal 2 -0.7. Tunable via env PR_RMULT for R-free. Also reinstates the pre-factored per-image orientation refinement (per-pixel ShoeboxResidual against the shoebox, regularised to the spot-centroid orientation, re-predict), behind env PR_ORIENT (off by default), to A/B its effect on serial-data R-free. On the jet CCref it is a no-op (XtalOptimizer orientation already at the optimum), but CCref is a weak R-free proxy here, so it is left for R-free validation. NOTE: PR_RMULT / PR_ORIENT are temporary diagnostic env knobs; the final multiplier value and the orientation-refine decision are to be fixed against R-free, then baked. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-14 09:18:09 +02:00
leonarski_f	bf6efc7fe9	Integration radius: default r1=4, CLI flag, PixelRefine shares the knob ... Bumped the default signal-box radius to r1=4 (r2=6, r3=8): on the lysozyme jet (1% DMM) it lifts CCref 50.1->52.2% and CC1/2 90.8->92.5% (its broadened spots spill past a radius-3 box), is neutral on the mono crystal and on the classical integrator. Added 'jfjoch_process --integration-radius <r1|r1,r2,r3>' (a single value derives r2=r1+2, r3=r1+4) and wired PixelRefine's shoebox radius to BraggIntegrationSettings::GetR1() so it shares the classical integrator's knob. (Explored but rejected: an elliptical/anisotropic Term-2 profile. The jet's tangential spots are mildly anisotropic - axis ratio 1.15->1.44 low->high res, azimuthal mosaic, separate from the radial DMM bandwidth - but using the measured 2x2 covariance as the profile DEGRADED the jet, CC1/2 92.5->83.5: the tight measured width loses to a generous aperture, same lesson as the radius bump.) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-13 23:27:36 +02:00
leonarski_f	100fe7b7e7	PixelRefine: make factored Terms 1+2 the model, remove old wiring ... PixelRefine is now an intensity-only operation: geometry is fixed (refined upstream by XtalOptimizer) and the only objective is the factored per-reflection likelihood (FACTORED_MODEL.md Terms 1+2) - measured per-resolution profile width R1 plus one Fisher-weighted intensity/scaling residual per reflection, fitting the per-image scale G and B. Validated on crystal 2 (fixed_master.h5 as stills, 1.7 A): CC1/2 84-92%, CCref 77-92%, flat - reproduces the env-flag prototype and matches the rotation path from the stills path. Removed: - the per-pixel ShoeboxResidual loss and PixelResidual cost functor; - all in-PixelRefine geometry refinement (orientation/cell/beam/distance/R), the regularised-orientation LSQ, signal-weighting, and the global sweep; - Term 3 (per-spot recentring) - a confirmed no-op on both crystals; - the diagnostic scaffolding (covariance, centroid, adaptive_R1) and the PR_* env knobs + stderr dumps in IndexAndRefine; - the PredictImage/ChiSquaredImage renderers and the entire viewer PixelRefine window/table/params + worker bindings + shoebox overlay. The sweep box-integrator background median became mean (consistency) by virtue of removing the sweep. METHODS.md rewritten for the current model; findings recorded in FINDINGS-2026-06.md. Net -2200 lines. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-13 22:02:18 +02:00
leonarski_f	6f2033db00	PixelRefine: checkpoint before cleanup (factored model + all diagnostic levers) ... Snapshot of the messy state: factored likelihood Terms 1+2+3 behind PR_* env flags (PR_INTENSITY/PR_SHAPE/PR_RECENTER) alongside the old per-pixel ShoeboxResidual, plus diagnostic scaffolding (PR_R0/R1/COV/FIX_R0/FIX_R/ ADAPT_R1/CENTROID/RECENTER) and the FACTORED_MODEL.md spec. Next commit makes Terms 1+2 the model and strips all of this. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-13 21:34:33 +02:00
leonarski_f	db68c8dc38	PixelRefine: Results seem to be much better	2026-06-12 17:28:18 +02:00
leonarski_f	bd5fef7f61	PixelRefine: Simplify (remove Lorentz correction, remove background from azimuthal integration)	2026-06-10 18:37:46 +02:00
leonarski_f	59281f6330	Revert "Bragg integration: option to use azimuthal integration profile" ... This reverts commit e4230bc14e.	2026-06-10 16:36:37 +02:00
leonarski_f	e4230bc14e	Bragg integration: option to use azimuthal integration profile	2026-06-10 14:41:36 +02:00
leonarski_f	6c85aaba2b	BraggPrediction: Include X-ray bandwidth	2026-06-09 15:01:44 +02:00
leonarski_f	e4b66f9cd9	PIxelRefine: Another iteration	2026-06-09 08:04:27 +02:00
leonarski_f	155c53acd8	jfjoch_process: First pixel refine integration	2026-06-08 15:37:27 +02:00
leonarski_f	cc3eb8352c	v1.0.0-rc.148 (#58) ... 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	2026-06-08 08:30:35 +02:00
leonarski_f	75de40f52b	v1.0.0-rc.147 (#57) ... 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_viewer: Add reciprocal space viewer * jfjoch_process: Two pass algorithm that does spot finding/indexing + integration of full dataset * jfjoch_process: Improve logic for rotation indexer, to make execution more deterministic (still work in progress) Reviewed-on: #57 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-06-02 11:49:24 +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	4878318c27	v1.0.0-rc.139 (#49) ... 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: Further reduce startup time for DECTRIS detectors by selectively modifying SIMPLON parameters on `/start` * jfjoch_broker: Further reduce startup time for DECTRIS detectors by not setting beam center and detector distance via SIMPLON API on '/start' * jfjoch_broker: Add an extra message to ZeroMQ puller ready to monitor Lite worklow preparation time * jfjoch_broker: Image buffer configuration is postponed for Lite receiver flow till start message is received * jfjoch_broker: Use nanoseconds internally for frame/image/readout time * jfjoch_broker: Extra messages added for receiver operation (to be removed after debugging finished) * jfojch_broker: Improve profiling of different data analysis steps * jfjoch_broker: Record integration reflection count * jfjoch_broker: Fix bug where ZeroMQ preview frequency was confusing time units (micro vs. milliseconds) * jfjoch_broker: Fix bug where '/wait_till_done' got deadlocked * jfjoch_writer: Fix confusion between NaN and zero in floating-point datasets **Breaking changes**: detector definition is now using nanoseconds to define minimum frame time, minimum count time and readout time. Reviewed-on: #49	2026-04-29 09:50:50 +02:00
leonarski_f	c1c170112c	v1.0.0-rc.136 (#45) ... 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: Improve logic regarding indexing architecture and thread pools (work in progress). Reviewed-on: #45	2026-04-20 11:54:33 +02:00
leonarski_f	6133da1377	v1.0.0-rc.133 ... 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: Use httplib for HTTP server instead of Pistache * jfjoch_broker: Drop OpenSSL support * jfjoch_broker: Base work for multi-lattice support in the future * Update dependencies to more recent versions (spdlog, HDF5, Catch2, httplib) Reviewed-on: #41	2026-03-26 20:50:33 +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
leonarski_f	27496b8207	v1.0.0-rc.122 (#29) ... This is an UNSTABLE release. * jfjoch_broker: Add thresholding to prefer shorter vectors after FFT * jfjoch_broker: Add experimental mosaicity estimation for rotation experiments (this is work in progress) * jfjoch_viewer: Display file opening errors * jfjoch_viewer: When loading files over DBus add retry/back-off till the file is available Reviewed-on: #29 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-12-16 15:27:40 +01:00
leonarski_f	b02c412d59	v1.0.0-rc.118 (#25) ... This is an UNSTABLE release and not recommended for production use (please use rc.111 instead). * jfjoch_viewer: Fix issue when HTTP sync silently disconnected when it was enabled when the broker was starting measurement. * jfjoch_broker: Add protections on time of geometry optimization and reduce rotation recalculations Reviewed-on: #25 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-12-06 20:05:30 +01:00
leonarski_f	31a357fa57	v1.0.0-rc.113 (#19) ... This is an UNSTABLE release and not recommended for production use (please use rc.111 instead). * jfjoch_broker: Improve handling of rotation indexing * jfjoch_broker: More information saved in CBOR end message (WIP) * jfjoch_writer: Save rotation indexing lattice parameters and Niggli class * jfjoch_viewer: Remove (for now) primitive cell information Reviewed-on: #19 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-12-02 09:29:22 +01:00
leonarski_f	06949caf1a	v1.0.0-rc.112 (#18) ... This is an UNSTABLE release and not recommended for production use (please use rc.11 instead). * jfjoch_broker: Experimental rotation (3D) indexing * jfjoch_broker: Minor fix to error in optimizer potentially returning NaN values Reviewed-on: #18 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-30 17:39:22 +01:00