9 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	37a8c8e24e	Rotation merge: drop rocking events with an overloaded pixel; capture uncertainty in the merge variance ... A saturated pixel in a spot means the brightest part of the reflection was not measured. The integration used to drop the peak frame's partial (its peak pixel is unreadable) and keep the flanks, so the combine extrapolated the event from its tails by the partiality model: on a strongly diffracting small-molecule crystal the strongest low-order reflections read 2-3x low and were the largest SHELXL misfits. XDS drops such a reflection (OVERLOAD); so does rugnux now. - Integration (CPU + GPU engines): a reflection is `overloaded` when a signal-disk pixel is saturated, or unreadable on this frame but not in the run's pixel mask - EIGER/PILATUS write their error value for a pixel they could not count, which the preprocessor turns into a masked pixel like a gap's. The engines now receive the PixelMask to tell the two apart (an earlier attempt that re-classified the marker as saturation in the preprocessor broke a dataset whose gaps are not in the file's mask). An overloaded reflection is kept with its box sum, unfitted, only so its event can be recognised. - Rotation combine (CPU + GPU): an event with any overloaded partial is dropped whole; counted in the log and the report (OBSERVATIONS_REJECTED_OVERLOAD=). The unmerged MTZ export drops it too. - Everything else that reads reflections leaves an overloaded one out: AcceptReflection (stills merge, per-image scaling), the post-refinement gather, the axial-row sums. - Capture uncertainty: the merge rebuilds each full's variance at the reflection's mean (counting_variance / ModelSigma) and dropped the capture term the combine had put into sigma, so a full extrapolated from part of its rocking curve merged at the weight of a whole one. Fulls now carry it (Obs::capture) and the rebuilt variance adds (capture * <I>)^2, host and device. SHELXL R1 on rugnux's own integration (harness), median fix -> this: citric acid .0648 -> .0420 (XDS .051; 221 events dropped, EXTI 1.02 -> 0.29), HEPES .0396 -> .0381 (184), aspirin 20 keV .0387 -> .0385 (6), aspirin 25 keV .0376 -> .0375 (5); metformin/nidppe/dnba/lalanine/cytidine no overloads, unchanged. YAG .116 -> .128 (87 dropped; its scale loop does not settle either way). Proteins and private subset: see the branch report. Tests: BraggIntegrationEngineCPU_SaturatedPeakIsFlaggedNotDropped (new), BraggIntegrationEngineGPU_MatchesCPU (overloaded flag compared), AcceptReflection_ResolutionLimits, [write_reflections], [large]. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 21:01:40 +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	90e804acd7	v1.0.0-rc.150 (#60) ... * jfjoch_broker: When in FPGA workflow (with PSI detectors) azimuthal integration might be forced to CPU - this will require more computational power, but it enables more integration bins and reports standard deviation of each bin. * jfjoch_broker: Raise error if one is in FPGA flow and there are too many azimuthal integration bins. Reviewed-on: #60	2026-06-15 20:24:15 +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	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	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	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
leonarski_f	061152279c	v1.0.0-rc.91	2025-10-20 20:43:44 +02:00