14 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	c86beeb393	rotation indexer: fix sub-range crash, explicit angle, settings + guards ... Running rotation indexing on a sub-range (e.g. images 60-120) segfaulted: the first pass passed the *global* image number to RotationIndexer::ProcessImage, which indexes v_ (sized to the run's image count) -> out-of-bounds write. - ProcessImage now takes an explicit mid-exposure angle (optional; falls back to the goniometer at the image index), so the indexer no longer assumes its slot index equals the goniometer image index. IndexAndRefine supplies it via RotationAngle(), matching the angle used for prediction. Added a bounds guard in ProcessImage so a bad index can never corrupt memory. - JFJochProcess feeds the rotation indexer the local ordinal (not the global index), and shifts the goniometer (start += start_image*incr, incr *= stride, per-image wedge preserved) so local index i maps to the angle of original image start+i*stride - fixing rotation angles for the whole sub-range pipeline (prediction, refinement, output), not just the indexer. - Expose "Rotation images" (number used for the first pass) in the job dialog, enabled when rotation indexing is on. (Count > available is already clamped by select_equally_spaced_image_ordinals.) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-22 15:59:21 +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	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	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	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	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