296 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Fable 5	347228d008	jfjoch_process: azimuthal-integration CLI + default 0.01 1/A q-spacing ... Add -q/--azim-q-spacing, --azim-min-q, --azim-max-q, --azim-phi-bins (mirroring jfjoch_azint) so offline processing can set the radial binning, applied before the azint mapping is built. Set the AzimuthalIntegrationSettings default spacing to 0.01 1/A (was 0.05): the coarse default barely resolved the narrow ice rings, diluting the ice-ring score. Finer binning sharpens it a lot with no effect on processing - EP_cs_01-17 ice score 4.6->7.3 (max 11->23), clean cytC stays ~1.0, and space group / cell / ISa / completeness are unchanged (cytC, InsI3, MyoB, pding4_001 verified full-image). Documented in JFJOCH_PROCESS.md. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>	2026-07-02 17:24:05 +02:00
leonarski_fandClaude Fable 5	5737d2e1d0	ice score: measure against a smooth whole-profile background, not shoulders ... The score's baseline was two adjacent shoulder bins with a bin-overlap bug - the ring's edge bins were counted in both the ring and the shoulder, since GetMeanValueOfBins is inclusive. At the typical (coarse) azint binning (dq ~ 0.05 in q, wider than the 0.03 ring half-width) a shoulder is only ~1 bin, so the ratio was noisy and poorly separated. Replace it with the ring intensity over a smooth whole-profile background: a running median of the non-ice bins, interpolated under each ring. Clean crystals now sit at ~1.0 and ice separates far more cleanly on /data/rotation_test: cytC 1.06->1.03, lysoC 1.23->2.77, EP_cs_01-17 1.67->4.51 (max 11.4). A z-score / abnormality probability was tried but is uninformative here - with many photons any real ice ring is highly significant, so the useful discriminator is the ice magnitude (this ratio), noted in CPU_DATA_ANALYSIS.md. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>	2026-07-02 17:05:39 +02:00
leonarski_fandClaude Fable 5	f422988cd2	ice score: per-image ice-ring indicator plumbed through all layers ... A single per-image ice_ring_score - the strongest hexagonal-ice ring band/shoulder intensity ratio from the azimuthal profile (1 = no ice) - computed in the CPU and FPGA analysis paths and the offline azint worker, then plumbed through every layer: DataMessage/EndMessage, CBOR (frame_serialize), HDF5 (/entry/MX/iceRingScore), ScanResult, receiver plots (PlotType::IceRingScore), the OpenAPI spec (plot_type + scan_result schema, with regenerated broker/gen and frontend client) and OpenAPIConvert, the reader + Qt viewer, and the React frontend plot. Documented in docs/CBOR.md, docs/HDF5.md and docs/CPU_DATA_ANALYSIS.md, with the general "add a per-image quantity" recipe added to CLAUDE.md. Verified in HDF5: lysoC (weak ice) mean 1.23, EP_cs_01-17 (heavy ice) mean 1.67 / max 2.23. This is a monitoring quantity - it does not gate scaling (which already excludes all ice rings) or merging (handled by the CC1/2 ring mask). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>	2026-07-02 16:37:12 +02:00
leonarski_fandClaude Fable 5	6ffb16f142	merge: mask ice rings whose CC1/2 collapses below their resolution neighbours ... An ice-contaminated ring decorrelates its reflections, so its merged half-set CC1/2 falls well below the Bragg trend of its resolution shoulders (e.g. EP_cs_01-17 2.25A ring CC1/2 0.12 vs shoulders 0.89). After the final merge, compute per-hexagonal-ice-ring CC1/2 in the ring band (+/- ice width in q=2pi/d) against the shoulders either side, mask any ring more than 0.05 below its shoulders (reliable shoulder CC1/2 > 0.5, >=20 reflections each) and re-merge without them. Weak/absent rings track their neighbours and stay, so clean crystals are untouched. Data-driven and robust on /data/rotation_test: 16/18 crystals mask nothing and are unchanged (every clean crystal, plus icy-but-fine EP_cs_02-10); EP_cs_01-17 masks 6 rings, CC1/2 6.9% -> 28%; CQ066/pding4_003 mask one marginal ring each. A well-scaled CC1/2 test, replacing the fragile per-image azimuthal cutoffs. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>	2026-07-02 16:06:39 +02:00
leonarski_fandClaude Fable 5	8c084021e6	ice rings: exclude from scaling, keep in the final merge (recover completeness) ... --detect-ice-rings previously dropped ice-ring reflections outright before scaling, which also removed them from the merge and gutted low/mid-resolution completeness on crystals that merge them fine (e.g. lysoC 80% -> the ice bands show as jagged shell completeness). Instead flag them (new Reflection.on_ice_ring, set in JFJochProcess, carried through the 3D combine) and exclude the flag only where a model is fit: the per-image scale (ScaleOnTheFly::Accept + the per-image CC), and - for the de-novo P1 pass - the space-group search and error model (MergeOnTheFly::ExcludeIceRings, on for for_search). The final in-symmetry merge and its statistics keep them, so completeness is preserved. /data/rotation_test battery vs the previous drop-from-merge behaviour: space group correct on all 18; completeness recovered broadly with CC1/2 and ISa held (cytC_2 82->99.7%, cytC_3 73->99.7%, InsI3 76->99.5%, lysoC 80->99.7%, MyoB 80->99.7%, InsH3 78->99%). Excluding ice from the P1 search merge is what keeps the space group correct: without it InsI3 flipped I23->P1 and EP_cs_01-17 P2->P1. Known limitation: on heavy-ice crystals (EP_cs_01-17) the strong ice is garbage and keeping it in the final merge collapses CC1/2 in the ice shells (91.7->6.9%). Distinguishing strong vs weak/absent rings per crystal needs data-driven, per-ring ice detection (azimuthal radial profile) - the planned next step. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>	2026-07-02 14:29:37 +02:00
leonarski_fandClaude Opus 4.8	ed9f6ac9eb	integration: remove --reciprocal-profile (proven per-frame dead-end) ... An 11-crystal mosaicity-stratified re-test (/data/rotation_test, off vs on vs a de-contaminated variant, plus a per-frame dump of the fitted widths) showed the dial is net-negative and cannot work in the per-frame paradigm: - The C|q|^2 mosaicity term - the whole point - is unfittable per-frame: the fitted curvature a2 comes out ~0 (often negative) on every crystal, with zero correlation to the XDS mosaicity (0.09..0.42 deg). Strong spots sit at low q where eta^2 q^2 is invisible; the curvature only appears at high q where there are ~0 strong spots. The law degenerates to a straight line. - With a2~0 the high-res width becomes a blind 1/cos^2(2theta) extrapolation, 2-4x wider than per-shell. The per-shell path's high-res "starvation" (flat narrow fallback) is accidentally correct: weak, crowded high-res spots want a narrow aperture, not the true wide spot shape. - The over-wide profile pulls background into weak spots -> R-meas rises, CC1/2 drops in reliable high-multiplicity shells (pding4_001, pding4_003, MyoB, EcwtCQ066). A cap at the widest well-sampled per-shell width recovers the regression, confirming over-widening is the harm. No crystal reliably wins; the apparent overall-CC gains were all in noise shells (mult 2-3, CC<20%). Delete the CLI flag, the BraggIntegrationSettings::reciprocal_profile setting, and the per-frame fit block. Default (per-shell) integration is byte-identical. NEXTGEN_INTEGRATOR.md records the finding as a dead-end for posterity. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-02 11:39:09 +02:00
leonarski_fandClaude Fable 5	7e3ad84a5b	jfjoch_process/scale: default to mmCIF, auto-detect rotation, rot3d partiality ... - Default reflection format is now mmCIF (ScalingSettings.h, the single source of truth). jfjoch_process and jfjoch_scale no longer hard-code a local MTZ default; they override only when --scaling-output is given. jfjoch_viewer inherits this. - A dataset with a rotation goniometer axis is processed as rotation data (two-pass indexing) by default; add --process-as-stills to force per-frame stills. -R still tunes the first-pass image count. - rot3d is the default partiality model for rotation processing (fixed for stills) when no explicit -P is given. - Update docs/JFJOCH_PROCESS.md: new de-novo rotation/stills examples, corrected -R/-P/--scaling-output defaults, --process-as-stills, and a real Integration table. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>	2026-07-02 08:34:50 +02:00
leonarski_fandClaude Opus 4.8	b7613c559c	smargon: write chi/phi goniometer position into NXmx transformations ... Add an optional Smargon static positioner (chi/phi angles + rotation axes) that is reconstructed into the NXmx sample transformation chain. Chi/phi are appended at the innermost end of the chain (closest to the sample) for both the goniometer and grid-scan branches, with axes defaulting to chi {0,0,1} and phi = omega default {1,0,0}. - SmargonPosition gains chi_axis/phi_axis (common/JFJochMessages.h) - OpenAPI: optional phi_axis/chi_axis arrays; clients regenerated - OpenAPIConvert wires Dataset_settings.smargon -> DatasetSettings - CBOR serializer/deserializer round-trip the axes - tests: CBORSerialize_Start_Smargon Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-01 11:45:08 +02:00
leonarski_fandClaude Opus 4.8	a74b8767de	ice rings: add --detect-ice-rings and exclude ice-ring reflections from scaling ... jfjoch_process gains --detect-ice-rings, which (a) activates the existing spot-finder ice flagging (ice spots de-prioritised in indexing) and (b) drops reflections sitting on a hexagonal-ice powder ring from scaling/combine/merge/stats, via a new shared IsOnIceRing() helper over ICE_RING_RES_A using the spot-finder's q half-width. Their integrated intensity is contaminated by the strong, variable ice background, so leaving them in mis-scales the whole frame and inflates the error model. On EP0117 (ice-ring crystal): de-novo space-group determination recovers from P1 to P2 and CC1/2 improves (31->37%). Off by default; a no-op without the flag. This is the first, non-controversial step - the residual gap needs ice-aware background/integration (follow-up). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-30 20:40:51 +02:00
leonarski_fandClaude Opus 4.8	0783af247c	scaling: express rot3d smooth-g as a rotation range in degrees (XDS DELPHI-like) ... --smooth-g now takes a rotation range in degrees (default 5) instead of a frame count, converted to an odd frame window from the oscillation step inside JFJochProcess. This makes the per-frame scale-G smoothing physical and independent of the frame slicing. (Note: G-smoothing is not the cure for the low-symmetry stochastic collapse - the per-image scale Cauchy loss is - but a degree-based window is the correct parameterization regardless.) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-30 20:00:53 +02:00
leonarski_fandClaude Opus 4.8	e45a1577d6	jfjoch_process: optional absorption surface for rot3d scaling (--absorption) ... Adds an opt-in smooth absorption correction for rotation scaling. After the rot3d fulls are scaled, --absorption[=num] fits a multiplicative surface A(s1_crystal) - a degree<=4 monomial basis (real spherical harmonics up to l=4, as XDS/DIALS) of the diffracted-beam direction in the crystal/goniometer frame, by ridge-regularized log-linear least-squares of I_scaled/I_ref weighted by (I/sigma)^2, over num iterations (default 3); the surface divides image_scale_corr and the fulls are re-merged. Off by default and a no-op without rot3d. On the test panel (~13 keV, thin crystals) it is metric-neutral - fitted rms(log A) ~3-4%, ISa/CC1/2 unchanged - because absorption is negligible there and the per-frame scale G(phi) already absorbs the angular part. It is kept as a lever for low-energy data (e.g. 6 keV) where absorption becomes significant. Stored as ScalingSettings::absorption_iter. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-30 15:23:01 +02:00
leonarski_fandClaude Opus 4.8	3aec235f67	integration: add --reciprocal-profile dial (global reciprocal-space width) ... The per-shell profile width is learned in pixels, so it varies ~4x with resolution (mostly the geometric projection of a near-constant reciprocal-space relrod) and must be binned per shell -> it starves at high resolution / on sparse data. The new --reciprocal-profile flag instead learns ONE global width in reciprocal space, sigma2_q,tan = A + B|q| + C|q|^2: the Jacobian g_tan=cos(2theta) removes the geometric projection, and C|q|^2 is the crystal mosaicity relrod (variance ~(eta|q|)^2). Applied per reflection as sigma2_tan,px = (A + B|q| + C|q|^2)/g_tan^2 (B,C clamped >=0; quadratic->linear->constant fallback). Off by default. On the sharp HEWL test crystal (mosaicity 0.091deg, so C fits to ~0 and it reduces to the validated linear form) it is metric-neutral: ISa 16.2->16.3, anomalous 0.92x unchanged, CCref band 90.0->89.9, CC1/2 a touch lower (per-shell isn't starved at 23k spots/shell, and a global fit is less flexible). So: simpler + more transferable at a small CC1/2 cost, ISa/anomalous held. Its payoff is on MOSAIC crystals (large C|q|^2), where per-shell starves on the wide weak high-res spots and 6 shells are too coarse; both lyso test crystals are sharp, so it ships as a dial to try on mosaic data elsewhere. A separate radial relrod fit was tried and dropped (no gain). See NEXTGEN_INTEGRATOR.md. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-30 14:26:08 +02:00
leonarski_fandClaude Opus 4.8	eccd10a0a7	integration: neighbour-mask the profile-fit background ring, widen r3 8->10 ... ProfileIntegrate2D::BoxSum now excludes every predicted reflection's r2 disk from the r2..r3 background annulus (mirroring BraggIntegrate2D), so a neighbour Bragg peak can no longer bias a reflection's background high and over-subtract. With neighbours excluded the annulus can safely widen, so the default r_3 goes 8 -> 10 (more background pixels, lower-variance estimate). Measured (rotation lyso @1.0 A, external CCref/CCxds vs XDS): 1.05 A CCref +1.3 / CCxds +1.3, R-meas -5 pts, low-res R-meas unchanged. Serial (Jet8 @0.0002 bandwidth): 1.68 A CC1/2 +3.9 / CCref +1.1, 1.58 A +4.0 / +1.6. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-29 22:41:14 +02:00
leonarski_fandClaude Opus 4.8	99b923e727	scaling: smooth per-frame scale G across frames before the rot3d combine ... ScaleOnTheFly fits each frame's scale G independently with no neighbour coupling, so the few partials of one rocking event are weight-summed in combine3D on inconsistent scales - jitter that never enters the full's counting sigma and instead surfaces as scatter between symmetry mates, inflating the error-model b (low ISa). A centered moving average of log(G) over a small frame window (default 9, on for rot3d) removes it, mirroring XDS's smooth scaling. Complementary to --scale-fulls (which rescales between fulls, after the combine): smoothing fixes within-event scale, scale-fulls fixes between-full. On the rotation lysozyme set (1.4A, merged, with --scale-fulls): ISa 11.7 -> 15.0, R_meas 10.0% -> 8.3%, CCref stable, chi2 ~0.97 (honest). Anomalous (full-res): ANODE S-peak 0.61x -> 0.80x of XDS. --smooth-g[=window] tunes/disables it (=0 off); --mosaicity <deg> is a diagnostic that fixes the scaling mosaicity for sweeps. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-29 19:02:47 +02:00
leonarski_fandClaude Opus 4.8	ed98775ba3	rot3d: capture-aware sigma for under-captured fulls + expose per-image scale ... The rot3d combine over-extrapolates fulls reconstructed from only a fraction f of their rocking curve (min_partiality admits f as low as 0.02). Against XDS on HEWL these low-capture fulls are systematically biased HIGH (+15% at f=0.8 to +100% at f=0.3), and the bias - not random scatter - is the strong-reflection floor that hurts anomalous accuracy. --capture-uncertainty <coeff> (default 0 = off, baseline bit-identical) adds a systematic uncertainty ~coeff*(1-f)*I to each full's sigma, so the merge down-weights the over-extrapolated fulls and the error model treats their scatter as expected. Unlike outlier rejection (which trades accuracy for CC1/2), this fixes a real bias, so accuracy improves: at coeff=1.0 the anomalous peak height vs XDS rises CL_CL +16%, SD_MET/SG_CYS +5-6%, ISa 10.7->11.0. Rotation- only (no-op for stills, which never combine). Also expose the per-image scale offline: Combine3D now carries the first-pass per-image scale metadata (G, B, mosaicity, wedge, CC) forward instead of dropping it, and jfjoch_process -M writes <prefix>_image.dat from it (the offline self-scaling result was otherwise unobservable - process.h5's per-image arrays are only filled on the online path). This enabled the XDS DECAY comparison (jfjoch G tracks XDS, r=0.93). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-27 19:41:20 +02:00
leonarski_fandClaude Opus 4.8	7e7a73062c	Compression: add BSHUF_ZSTD_RLE_HUFF (RLE runs + Huffman literals) ... New CompressionAlgorithm that emits a standard Zstandard frame: zero/0xFF runs become RLE_Blocks (like BSHUF_ZSTD_RLE) and literal regions become Compressed_Blocks with per-block adaptive Huffman literals and no sequences (Number_of_Sequences=0). Short runs are absorbed into the literal stream; incompressible literals fall back to Raw_Blocks so the worst case stays within ZSTD_compressBound. The Huffman tree + bitstream are produced by zstd's own HUF_compress{1,4}X_repeat (the same calls ZSTD_compressLiterals uses); only the frame/block/literals-section framing is hand-written, with comments citing zstd_compression_format.md so it can be checked clause by clause. Output decodes with stock ZSTD_decompress, so no reader changes are needed (decode routes like BSHUF_ZSTD). On sparse diffraction this gives ~12% smaller files than bitshuffle/LZ4 at about the same end-to-end speed, sitting between LZ4 and full ZSTD; for maximum ratio use BSHUF_ZSTD. Robust on any input: tests round-trip pure zeros, Poisson(10), Mersenne-Twister noise (checked against the size bound), an extreme-sparsity mask, and a real lyso image through stock ZSTD_decompress. API: exposed as "bszstd_rlehuf"; regenerate the Python/TS clients (update_version.sh) to surface the new value there. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-27 14:41:46 +02:00
leonarski_fandClaude Opus 4.8	02514bb6b7	Compressor: throw on overflow instead of returning a negative size ... Compress() and FrameTransformation::CompressImage() returned int64_t with a negative value meaning "did not fit". That is a footgun: the negative result silently converts to a huge size_t if a caller forgets to check it. Return size_t and instead throw a named CompressionBufferTooSmallException (deriving from JFJochException, Compression category) when the output would not fit the destination buffer. The receiver catches it explicitly and drops just that frame, as before; the offline/GetCompressedImage path uses a worst-case buffer so it never throws. Add a test that a too-small destination throws and a worst-case buffer does not. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-27 08:17:21 +02:00
leonarski_fandClaude Opus 4.8	2398330e52	Drop oversized-metadata frames instead of aborting the collection ... A serial-crystallography run on a detector with a large converted geometry (JF17T16, modules tiled vertically + horizontally) aborted with "Array out of bounds (Not enough memory to save image)". An indexed still on such a detector predicts/integrates close to the kMaxReflections (10000) cap; at ~170 B per serialized Reflection that is ~1.7 MB of per-image CBOR metadata, which overflowed the fixed 1 MB the buffer slot reserved on top of the image. The serialization guard then threw and cancelled the whole run. - Raise the per-image metadata headroom from 1 MB to 4 MB (GetImageBufferLocationSize). The worst case - 10000 reflections + 2000 spots (API max) + 65534 azimuthal bins - serializes to 2.78 MB, leaving margin while staying negligible next to the multi-MB image slot. - When metadata still does not fit, drop just that frame (log metadata/image/slot sizes + recycle the slot) instead of aborting, in both the FPGA and Lite receivers. - Add a regression test asserting the worst-case metadata fits the headroom. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-26 17:11:41 +02:00
leonarski_fandClaude Opus 4.8	786af96b3b	SearchSpaceGroup: POINTLESS-style rewrite, pipeline integration, twinning test ... Space-group search (image_analysis/scale_merge/SearchSpaceGroup): - Two-stage POINTLESS-style determination. Stage A scores each distinct rotation operator once (was once per candidate space group, ~34x faster on lysozyme: ~26s -> <1s) and picks the largest point group all of whose operators confirm. Stage B picks the maximal space group whose predicted absences are confirmed weak, fixing the prototype's default to the symmorphic group (it returned P422 instead of P4(3)2(1)2). Enantiomorphic / origin-ambiguous pairs (P4(1) vs P4(3), I222 vs I2(1)2(1)2(1)) are reported as indistinguishable. - Constrain candidates to subgroups of the lattice (metric) holohedry and weigh centering only P-vs-metric, fed from rotation indexing's LatticeSearch result. Integration / pipeline: - With no user-fixed space group, predict in P (IndexAndRefine) so the centering-absent reflections are integrated and the search can confirm/deny centering (catching pseudo-centering / a missed superstructure) instead of trusting the metric; a user-fixed group still rejects absences in integration. - JFJochProcess: scale+merge in P1 -> determine the space group -> set it and re-scale+merge in it (statistics then come out in the right symmetry) -> write it to /entry/sample/space_group_number (new EndMessage.space_group_number, preferred by NXmx::Sample). jfjoch_scale no longer searches; it consumes the file's space group (and no longer clobbers it with an empty -S). Twinning (new image_analysis/scale_merge/TwinningAnalysis): Padilla-Yeates L-test (<|L|>, <L^2>; acentric-only, positive intensities so L is bounded) plus a shell-normalised <I^2>/<I>^2 second moment and a twin-fraction estimate. Reported after the final merge in jfjoch_process and jfjoch_scale, and surfaced in the jfjoch_viewer merge-statistics window with a red outline when twinning is suspected. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-26 16:11:28 +02:00
leonarski_f	54c667190f	v1.0.0-rc.155 (#65) ... 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: Remove pixelrefine option (replaced with ProfileIntegrate2D) * jfjoch_viewer: Some graphical improvements. * jfjoch_viewer: Simplify und unify data analysis settings. * jfjoch_writer: Add TCP keepalive to increase robustness if jfjoch_broker "dies" in the middle of data acquisition. Reviewed-on: #65	2026-06-25 22:01:48 +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	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	2026-06-17 20:36:24 +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	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	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	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>	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	2026-04-30 22:16:50 +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	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_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	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	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	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>	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	2026-04-09 13:30:47 +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	1c4dfd03e2	v1.0.0-rc.123 (#30) ... This is an UNSTABLE release. * jfjoch_broker: Use newer version of Google Ceres for (potential) CUDA 13 compatibility * jfjoch_broker: Improve performance of generating preview images, especially for large detectors (9M-16M) * jfjoch_viewer: Improve performance of displaying images, especially for large detectors (9M-16M) * jfjoch_viewer: Add more color schemes for better image readability * HDF5: Common mutex for reading and writing HDF5 if both operations were to happen in the same executable * HDF5: suppress warning if path (upstream group) doesn't exists when checking if leaf exists Reviewed-on: #30 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-01-30 13:43:09 +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	e2b240356c	v1.0.0-rc.121 (#28) ... This is an UNSTABLE release. * jfjoch_broker: Report changes in the image buffer, so viewer doesn't reload constantly * jfjoch_viewer: Improve performance of loading images * jfjoch_viewer: Auto-throttle image loading in HTTP-sync / movie modes * jfjoch_viewer: Auto-foreground calculated with histogram * jfjoch_viewer: Fix rare segmentation fault Reviewed-on: #28 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-12-12 21:24:20 +01:00
leonarski_f	a0a659a02c	v1.0.0-rc.120 (#27) ... This is an UNSTABLE release. * jfjoch_broker: Improve performance of binary plot export Reviewed-on: #27 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-12-09 15:21:40 +01:00
leonarski_f	36d0507758	v1.0.0-rc.119 (#26) ... This is an UNSTABLE release and not recommended for production use (please use rc.111 instead). * jfjoch_broker: Add binary export of data analysis plots over OpenAPI * jfjoch_broker: Minor fixes to HTTP error handling * jfjoch_viewer: Prefer binary plots over JSON plots * jfjoch_viewer: Change foreground with F button + wheel * jfjoch_viewer: Change way how angles are displayed * jfjoch_viewer: Display resolution of the mouse cursor in top left corner Reviewed-on: #26 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-12-08 19:53:35 +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
leonarski_f	05410d7cb3	v1.0.0-rc.109 (#15) ... This is an UNSTABLE release. * jfjoch_viewer: Add keyboard shortcuts and option to copy image to clipboard * jfjoch_broker: Fix bit-width and exposure time for PSI EIGER detectors Reviewed-on: #15 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-26 13:48:59 +01:00