1118 Commits

This Branch

This Branch

All Branches

Author	SHA1	Message	Date
leonarski_f	1a03e884c4	CHANGELOG: adjust	2026-06-25 20:48:52 +02:00
leonarski_f	0a71d76b0f	VERSION: 1.0.0-rc.155	2026-06-25 20:47:45 +02:00
leonarski_f	884e831359	TCPImagePuller: add OS-level TCP keep-alive	2026-06-25 20:44:42 +02:00
leonarski_fandClaude Opus 4.8	4462f0998d	Viewer: single "Process as stills" mode + compact, folded panel ... Replace the scaling partiality combo + "3D rotation scaling" checkbox with one "Process as stills" checkbox in the indexing section (enabled only for rotation datasets, unchecked by default). Unchecked on a rotation dataset drives the full rotation path (rotation indexing at 60 first-pass images, Rotation partiality, rot3d combine, scale-fulls); checked treats it as stills (fixed partiality, per-frame indexing). The Analyze-dataset dialog drops its rotation options (the panel is the single source) and buildConfig reads rotation indexing from the experiment. Fix: the worker's UpdateSpotFindingSettings copied indexing fields one by one and was dropping RotationIndexing, so the mode never reached jobs. Also: fold the panel accordions on start except Geometry and Unit cell, and make the scaling resolution-limit a compact checkbox + field aligned with the other checkboxes. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-25 20:43:04 +02:00
leonarski_fandClaude Opus 4.8	383072ac80	Consolidate viewer settings into the panel + add the merge-stats window ... Make the inline settings dock the single home for processing settings and retire the separate Processing-settings window (and the dock<->window sync): - "Analyze image" / "Analyze dataset" move to the top of the panel; the MX/AzInt toggle decides the dataset-job kind, so the job dialog drops its mode combo. - The panel gains the most-used spot-finding (max spots, high-resolution, min pixels), Bragg (Gaussian profile-fit, r1/r2/r3) and scaling (partiality, "3D rotation scaling" = rot3d combine + scale-fulls, merge Friedel, refine B, resolution limit) handles, a live indexing-algorithm description line, and now owns the Bragg/Scaling settings. The now-unused window tab classes are deleted. - Complete the PixelRefine removal on the viewer side (the "Pixel refinement" option + profile-multiplier widget), fixing the transient HEAD breakage. New JFJochMergeStatsWindow: an analysis pop-up for a finished merge (hero numbers over a per-resolution plot / per-shell table), auto-opened on completion and reopenable from the processing-jobs dock. Fixes: disable tear-off dock floating (a floated dock is a dead off-screen window under WSLg, which has no window manager); version the saved dock layout so a stale arrangement is discarded instead of restoring a broken one; keep the Analyze-button icons; right-align and equal-width the stats table; line-plot / table toggle icons (ToolbarIcons gains linePlot + table). Add ScalingSettings::HighResolutionLimit_A(optional) so the panel can clear the resolution limit. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-25 20:43:04 +02:00
leonarski_fandClaude Opus 4.8	eab1bfab7d	Update viewer icons from the new jfjoch.svg logo ... Regenerate jfjoch.png (256-wide, transparent), jfjoch.ico (multi-resolution 16/32/48/64/128/256, square) and jfjoch.icns (16-512) from the new transparent-background jfjoch.svg, and add the SVG as the source. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-25 20:43:04 +02:00
leonarski_fandClaude Opus 4.8	38ea0ec237	Remove the experimental PixelRefine integrator ... On the LysozymeJet5 serial stills the default Gaussian profile-fit integrator (ProfileIntegrate2D) + reference scaling matched or beat whole-PixelRefine on every per-shell CC1/2 (overall 95.7% vs 91.9%), ISa (1.6 vs 1.2) and R-meas (98.5% vs 175%), with CCref a tie -- so PixelRefine has no remaining advantage. Reference-based per-image scaling is integrator-agnostic (IndexAndRefine::ReferenceIntensities builds a ScaleOnTheFly(experiment, reference) applied to any integrator's output), so the reference-dataset feature (CCref + reference scaling) is kept. Delete image_analysis/pixel_refinement/, GeomRefinementAlgorithmEnum:: PixelRefine and its gates, BraggIntegrationSettings::ProfileMultiplier (PixelRefine-only; R1 is shared and kept), and the -r pixelrefine / --profile-multiplier CLI. The inherited lessons (mean background, de-biased variance, tight-profile-loses / centroid floor, R-refinement futile) are folded into NEXTGEN_INTEGRATOR.md. NOTE: this transiently breaks the viewer build -- the committed viewer still references the removed enum and ProfileMultiplier. It is fixed in the next commit (the viewer feature work), held separate while the viewer UI is being tested. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-25 20:43:04 +02:00
leonarski_fandClaude Opus 4.8	18d9c8ad63	Fix anomalous completeness approaching 200% ... In anomalous mode (Friedel mates kept separate) unique_reflections counts I+ and I- of each acentric reflection as two unique members, but the possible-reflection count used the merged ASU, so completeness approached 200%. Count each acentric possible reflection twice (centric once) when not merging Friedel mates, matching how unique_reflections is counted; verified overall completeness 99.7% on the HEWL rotation set. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-25 20:43:04 +02:00
leonarski_fandClaude Opus 4.8	6e3c52bf91	Document the integrator and the XDS-quality investigation ... Rewrite NEXTGEN_INTEGRATOR.md from the early design draft into a full record: the diagnosis (our intensities are accurate and unbiased per ANODE, ~2x noisier than XDS), the experiment ledger of what worked and the many dead ends, the reusable tooling, and an honest assessment of the remaining gap. Fix the stale ProfileIntegrate2D.h header (it is wired and the default integrator, not a draft). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-25 20:43:04 +02:00
leonarski_fandClaude Opus 4.8	c84d581d3e	Remove the global (joint) scaling path ... Profiling showed the joint Ceres solve took ~120 s versus ~3.5 s for the alternating per-image scaling loop (~35x) for no quality gain (HEWL anomalous 0.54x vs 0.53x), so it is not worth keeping. Drop GlobalScale.{h,cpp}, the jfjoch_process --global-scale flag, and ScalingSettings::GlobalScaling. While here, in the same scaling/process area: fold scale_fulls into ScalingSettings (alongside combine_3d) so the CLI and experiment carry it uniformly, add per-substep [timing] logging to the scaling/merge post-pass (including the serial MergeAll vs parallel ScaleAllImages split), and carry structured MergeStatistics + ISa in ProcessResult. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-25 20:43:04 +02:00
leonarski_fandClaude Opus 4.8	a37613690e	Default two-pass rotation indexing to 100 first-pass images (was 30) ... A larger first-pass image set gives a more stable consensus lattice and so better per-frame prediction. On HEWL crystal 2 (full 360 deg) this lifts the anomalous S-peak height vs XDS from 0.57x to 0.61x and ISa from 10.5 to 11.0, at negligible cost (the first pass is a small fraction of the run). ~100 is the sweet spot; more (300) does not help further. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-25 20:43:04 +02:00
leonarski_fandClaude Opus 4.8	8d0cd19e48	Add XDS-order scaling of the rot3d fulls: --scale-fulls ... The rot3d combine emits fulls with partiality == 1 and image_scale_corr == 1, so the fulls are only ever scaled as per-frame partials upstream - their per-frame scale G is fit through the rocking-curve/partiality model (G*partiality*B*lp*Itrue - Iobs) and so absorbs any model error. XDS/DIALS instead scale the 3D-integrated fulls directly. --scale-fulls inserts a second scaling pass on the combined fulls with the Unity model (G*Itrue - I_full, no partiality term), between Combine3D and MergeOnTheFly, reusing ScaleOnTheFly on a Unity-configured experiment copy. It is a pure post-correction (updates the fulls' image_scale_corr 1 -> 1/G, no re-combine). HEWL crystal 2, anomalous S-peak height vs XDS: 0.53x -> 0.57x and ISa 9.4 -> 10.5 - improving precision and accuracy together (not the CC1/2-up / anomalous-down trade-off of outlier rejection). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-25 20:43:04 +02:00
leonarski_fandClaude Opus 4.8	50ebf1694e	Add global (joint) scaling path: jfjoch_process --global-scale ... Refine all per-image scales, per-image mosaicities and the shared per-HKL true intensities (plus the global wedge) together in one Ceres problem (GlobalScale.{h,cpp}, GlobalScaleCeres), as an alternative to the existing alternating merge-then-scale-each-image loop. The result feeds back into each reflection's image_scale_corr exactly as ScaleOnTheFly does, so the rot3d combine and MergeOnTheFly run unchanged and every metric stays comparable. On HEWL crystal 2 the joint fit converges to the same place as the alternating loop (anomalous S-peak vs XDS 0.53x -> 0.54x, ISa 9.4 both), confirming the alternating path already reaches the joint optimum. Kept as a validated alternative and the home for future global corrections. A shared quadratic absorption surface in detector position was prototyped here and dropped: it fit large non-physical coefficients (radially degenerate with the per-HKL resolution structure), lowered the scaling-fit residual but raised the error-model b (ISa 9.4 -> 7.3) and did not improve anomalous accuracy. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-25 20:43:04 +02:00
leonarski_fandClaude Opus 4.8	2041ce2bd5	Reject the +/-1 masked/saturated sentinel band in 2D integration ... Masked/error pixels carry the int type minimum and saturated the maximum, but the lossy codec can nudge them inward by one (masked observed as INT32_MIN+1 in the decompressed data). The integrators only checked the exact extremes, so a shifted sentinel in a reflection's background ring was treated as a valid pixel -> garbage background and intensity for any reflection whose box clips a module gap. Reject the +/-1 band too (real calibrated counts never approach the type extremes). Neutral on the well-centred lyso test set; a correctness fix for gap-clipping reflections. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-25 20:43:04 +02:00
leonarski_fandClaude Opus 4.8	7cc418ed2f	Add anomalous-accuracy scoreboard (HEWL ANODE vs XDS) ... One command to score a jfjoch anomalous merge against XDS on physical accuracy: feed the -A merge through SHELXC + ANODE (run under qemu-user, since this WSL2 kernel's vsyscall=none breaks the static SHELX binaries) and report <d"/sig> per shell and the averaged anomalous peak height at the model S/Cl sites vs XDS. Unlike R-meas/CC1/2 (precision) it catches accuracy regressions - e.g. outlier rejection raises CC1/2 but lowers the anomalous peaks. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-25 20:43:04 +02:00
leonarski_fandClaude Opus 4.8	9ba2401b53	Default to the Gaussian profile-fit integrator ... The Gaussian profile-fit (ProfileIntegrate2D) recovers more accurate intensities than the classical box-sum. On the HEWL rotation set its ANODE anomalous peak heights at the S/Cl sites rise from 0.46x to 0.53x of XDS (Met-S 6.0->7.1 sigma, Cys-S 5.6->6.1) and ISa 8.4->9.4, with R-meas unchanged. Box-sum stays available via --integrator boxsum. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-25 20:43:04 +02:00
leonarski_fandClaude Opus 4.8	e4b3064254	Scaling: reference dataset, 3D combine (-P rot3d), R-meas, profile-fit integrator ... Reference dataset (a): LoadReferenceMtz adds column selection + cell/SG/resolution + a data-vs-reference consistency check; jfjoch_process/jfjoch_scale gain --reference-column; the viewer gets a Reference section in the MX settings dock (worker-owned, independent of the loaded dataset) that flows into reprocessing jobs. 3D combine (-P rot3d): Combine3D weight-sums a reflection's per-frame partials into one counting-limited full before merging (orthogonal ScalingSettings::combine_3d flag, not a partiality model), with a de-biased Poisson variance. Crystal 2: ISa 1.7->8.4, R-meas ~67%->18.9%, intensities unchanged (CCref held). Quality metrics (b): R-meas (Diederichs-Karplus) + redundancy columns in MergeStats; ISa logged. jfjoch fulls 18.9% vs XDS 4.5% (same ASU/run). Profile-fit integrator (experimental): ProfileIntegrate2D (--integrator gaussian|empirical) is a reference-free, rot3d-compatible profile-fit extraction (the decomposed PixelRefine intensity step). Gaussian: R-meas 18.9->14.6%, ISa ->9.5. Anisotropy/per-region add nothing (the discriminating info is in the discarded rocking direction). See NEXTGEN_INTEGRATOR.md. --dump-observations exports the unmerged fulls for XDS comparison. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-25 20:43:04 +02:00
leonarski_f	6136f858af	v1.0.0-rc.154 (#64) ... 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_broker: Fix to TCP file pusher (remove kernel zero copy to improve reliability) Reviewed-on: #64 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.154	2026-06-25 18:12:00 +02:00
leonarski_f	75e401f0e5	v1.0.0-rc.153 (#63) ... 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_broker: Add EXPERIMENTAL pixelrefine mode for image processing * jfjoch_broker: Allow to load user mask from 8-bit and 16-bit TIFF files * jfjoch_broker: Add ROI calculation in non-FPGA workflow * jfjoch_broker: Fixes to TCP image pusher * jfjoch_broker: Remove NUMA bindings * jfjoch_broker: Improvements to indexing * jfjoch_broker: For PSI EIGER, trimming energies are taken from the detector configuration (now compulsory) instead of hardcoded values * jfjoch_writer: Save ROI definitions and the per-pixel ROI bitmap in the master file; azimuthal ROIs support phi (angular) sectors * jfjoch_viewer: Major redesign with dockable panels and saved layouts, plus on-canvas creation/move/resize of box, circle and azimuthal ROIs * jfjoch_viewer: Run jfjoch_process reprocessing jobs from inside the GUI and overlay per-run results Reviewed-on: #63 1.0.0-rc.153	2026-06-23 20:29:49 +02:00
leonarski_f	c49bd2ac3b	v1.0.0-rc.152 (#62) ... * jfjoch_broker: Fix bounds for azimuthal integration for Q spacing (allow Q of 1e-5) * jfjoch_viewer: Adjust Q bounds for azimuthal integration * jfjoch_azint: Add tool to do quick azimuthal integration Reviewed-on: #62 1.0.0-rc.152	2026-06-17 20:36:24 +02:00
leonarski_f	ef52dac2ee	v1.0.0-rc.151 (#61) ... * jfjoch_broker: For PSI EIGER detector allow to disable individual half-modules by putting empty hostname Reviewed-on: #61 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.151	2026-06-16 14:13:29 +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 1.0.0-rc.150	2026-06-15 20:24:15 +02:00
leonarski_f	ea575f790a	v1.0.0-rc.149 (#59) ... * XDS plugin: Fix HDF5 mutex to run on multiple processors Reviewed-on: #59 1.0.0-rc.149	2026-06-13 21:27:41 +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 1.0.0-rc.148	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 1.0.0-rc.146	2026-05-28 18:48:35 +02:00
leonarski_f	75f1c5f954	SHIM library improvements from the HDF Group	2026-05-08 11:39:51 +02:00
leonarski_f	caef26873e	v1.0.0-rc.145 (#55) ... This is an UNSTABLE release. The release has significant modifications for HDF5 writing logic - in case of troubles go back to 1.0.0-rc.144. * **Default HDF5 writing mode is with VDS, not soft-links** - this improves DIALS compatibility and makes format more future-proof, NXmx legacy format might be phased-out in the future. * XDS plugin: Improve performance of VDS reading. * jfjoch_writer: Significant improvement on how file systems I/O are handled through a dedicated pass-through VFD. * jfjoch_writer: Clean-up of HDF5 routines to better handle issues. Reviewed-on: #55 1.0.0-rc.145	2026-05-06 21:50:02 +02:00
leonarski_f	7d34e8a049	v1.0.0-rc.144 (#54) ... 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 performance of preview JPEG image generator at receiver startup (saving about 150 ms on measurement start for 16M) Reviewed-on: #54 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.144	2026-05-01 17:06:36 +02:00
leonarski_f	6e0bb971ac	v1.0.0-rc.143 (#53) ... 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: Avoid copying gain calibration together with DiffractionExperiment Reviewed-on: #53 1.0.0-rc.143	2026-04-30 22:16:50 +02:00
leonarski_f	87fde1b32e	v1.0.0-rc.142 (#52) ... 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. * Support for newer CUDA architectures (notably Blackwell); minimum CUDA version 12.8 * Minor changes to jfjoch_process, jfjoch_fpga_test and jfjoch_lite_perf_test to make them more consistent Reviewed-on: #52 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-30 16:47:53 +02:00
leonarski_f	d760b12a18	v1.0.0-rc.141 (#51) ... 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: Azimuthal integration mapping is generated with parallel computations, significantly reducing setup times * frontend: Fix selection of FFTW in indexing settings Reviewed-on: #51 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-30 13:04:54 +02:00
leonarski_f	239a441ee6	v1.0.0-rc.140 (#50) ... 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: For DECTRIS detectors, ZeroMQ link is persistent, to save time for establishing new connection * jfjoch_broker: Minor bug fixes for rare conditions Reviewed-on: #50	2026-04-29 21:40:22 +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 1.0.0-rc.139	2026-04-29 09:50:50 +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> 1.0.0-rc.138	2026-04-27 19:56:14 +02:00
leonarski_f	c981e1b91c	v1.0.0-rc.137 (#46) ... 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: Better track time for each operation in the processing stack * jfjoch_broker: Rewrite preprocessing of diffraction images in the non-FPGA workflow to better use GPUs (work in progress) * jfjoch_broker: Remove ROI calculation in the non-FPGA workflow (work in progress) * jfjoch_viewer: Toolbar displays image number starting from 1 (instead of 0) Reviewed-on: #46 1.0.0-rc.137	2026-04-25 19:59:21 +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 1.0.0-rc.136	2026-04-20 11:54:33 +02:00
leonarski_f	bb9f5c715f	v1.0.0-rc.135 (#44) ... 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. * Multiple small bug fixes scattered across the whole code base. (detected with GPT-5.4) * jfjoch_viewer: Improve image render performance Reviewed-on: #44 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.135	2026-04-16 11:59:59 +02:00
leonarski_f	4a852b4d6b	v1.0.0-rc.134 (#43) ... 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: Add better locking for detector object - should help, when detector initialization takes too long * jfjoch_writer: Enable writing single, integrated HDF5 file with both data and metadata * XDS plugin: Add generation of Jungfraujoch plugin for XDS * CI: Add tests with XDS and DIALS (`xia2.ssx`) Reviewed-on: #43 1.0.0-rc.134	2026-04-09 13:30:47 +02:00
leonarski_f	81bd9a06a1	CI pipeline upgrade (#42) ... Updates to CI pipeline * New docker image for Ubuntu 22.04 with CMake 3.26 * New docker image for Rocky 9 with DIALS 3.27 * New automated test to check for DIALS processing with xia2.ssx Reviewed-on: #42	2026-03-28 20:06:23 +01:00
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 1.0.0-rc.133	2026-03-26 20:50:33 +01:00
leonarski_f	2ab9deb20b	v1.0.0-rc.123 (#40) ... Documentation update Reviewed-on: #40 1.0.0-rc.132	2026-03-12 12:17:11 +01:00
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 1.0.0-rc.131	2026-03-07 11:34:04 +01:00
leonarski_f	928789a67c	v1.0.0-rc.130 (#37) ... 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: Rotation indexer has two retries if failes * jfjoch_broker: Rotation indexer handles small number of rotation images (like test shot) * jfjoch_broker: Integration calculates background mask based on R2 radius * jfjoch_process: HDF5 files are not saved by default Reviewed-on: #37 1.0.0-rc.130	2026-03-06 14:38:56 +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> 1.0.0-rc.129	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> 1.0.0-rc.128	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 1.0.0-rc.127	2026-03-02 15:57:12 +01:00
leonarski_f	32b681e591	v1.0.0-rc.126 (#33) ... This is an UNSTABLE release. If things go wrong with analysis, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Fix bug for monoclinic space groups being wrongly refined when beta is much different from 90 deg. Reviewed-on: #33 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.126	2026-02-19 07:01:38 +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> 1.0.0-rc.125	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> 1.0.0-rc.124	2026-02-01 13:29:33 +01:00