158 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	f0cdb027e1	Ice: default the merge mask off, gate the radial background on smooth ice, and pick detection by geometry ... Three defaults, each settled by measurement rather than by argument. The arbiter throughout is structure-referenced - anomalous peak height where a crystal can carry it, and otherwise the agreement of the ice bands with a fixed external model against resolution-matched DECOY bands carrying no ice. The band-versus-decoy contrast is used because R-free here tracks completeness, and every one of these switches moves completeness. The damage is real and it localizes: over the rotation battery the ice bands' excess amplitude reaches +9.6% on a smooth-ice crystal and +35% on the worst, while a clean control sits at +0.6% (z +0.45). On the worst crystal, nine of the ten largest excess peaks in a q scan land on hexagonal ring positions. Turning ice handling off leaves the contrast unchanged and forcing it on a clean crystal does not create one, so it is the ice and not the machinery. MERGE-TIME RING MASK -> OFF. It deletes reflections, which no other program does by default - AIMLESS, DIALS, xia2, XDS and CrystFEL all keep ice-band reflections in the merge and exclude them only from the model fit; autoPROC is the sole exception. On the one battery crystal where the mask fires and an anomalous arbiter can score it, dropping the band moved the mean peak height at the known sites by -0.001 +- 0.018 sigma, 2% of the site height, while removing 1149 unique reflections whose mean I/sigma was 3.62 against the dataset's own 3.05 - better than average data - and costing 17 completeness points in that shell. It fires on 5 of 37 crystals, changes no space group, and those 5 disagree in sign: it clearly helps the two most heavily iced, is a wash on two and costs a third. So it stays as a switch, worth setting by hand on a badly iced crystal where it shows in the high shell, but it is not a default. RADIAL BACKGROUND -> AUTO, gated per image. The correction models the background as a function of radius alone, and that is exactly when it works. On a crystal with pure smooth powder ice it removes 43% of the bands' excess amplitude, with the improvement 7x larger inside the bands than outside; on a crystal whose ice is discrete crystallite spots - no smooth ring to model - the excess amplitude GREW by half; on clean data it is inert to four decimals. The two ice channels already separate those morphologies, so --background-radial takes on|off|auto and auto applies it to an image when that image's peak-excluded score reaches --ice-min-score. Auto never engages without such a score, because the plain profile carries the Bragg peaks and cannot support an absolute threshold. Per image rather than per run, and that was tested rather than assumed: the gate fires on 100% and 94% of frames on the two crystals that want it, and on 1.5% of frames - 32 blocks, 23 of them single frames - on the textured-ice crystal. A seam statistic against off + f*(on - off) is null on both mixed runs, every merge statistic is bracketed by the pure arms, and the textured crystal's auto arm lands on `off` rather than on `on`'s harm. A run-level gate would need the score before the pass that integrates, i.e. rotation-only plumbing, and buys nothing measurable. The kernel was already built unconditionally, so flipping the flag per image is free - except on the GPU, where the launches were gated on a construction-time n_rad. That is why the buffers are now allocated whenever the correction could run, and Run() decides per image. DETECTION -> the geometry's default when the file is silent: on for rotation, off for stills, with the command line and then the file taking precedence. A rotation sweep sits on the same rings for the whole run, so ice there is a coherent systematic and the presence gate keeps it inert on a clean crystal; a serial stills run has too few spots per image to spend any on flagging. The master file's key is kept as written rather than collapsed to a bool, so "the file said nothing" is distinguishable from "the file said no" - it used to fall silently to off, taking the exclusion from the scale fit with it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-06 19:06:30 +02:00
leonarski_fandClaude Opus 5	09fb8e0306	Bragg integration: clip the background ring high side instead of trimming it ... The r2..r3 background ring was averaged with a 10% SYMMETRIC trimmed mean. A symmetric trim is not a consistent estimator of the mean of a right-skewed (Poisson) sample: on a clean Poisson ring it sits ~0.1 ct/px BELOW the true mean at every level, and with ~50 signal pixels in the r1 disk that under-subtraction adds ~5 counts to every partial on every frame. Measured two independent ways on four rotation datasets - stored background_mean against a plain ring mean over the same pixels on reflection-free frames, and directly on apertures that provably hold no reflection. Empty-aperture pedestal, counts: plain mean -0.03..-0.20, 10% symmetric trim +5.05..+6.34, 4 sigma clip +0.02..+0.54. Replace it with a high-side-only sigma clip at mean + n*sqrt(mean), n = 4 for monochromatic data. It rejects the same one-sided contamination the trim was there for - better, in fact: a 40 px neighbour core at +100 ct shifts the trim by +10.1 ct/px, because a symmetric trim collapses once contamination exceeds ~10% of the ring, versus +0.009 ct/px at 4 sigma. False rejection on a clean ring is 0.04-0.39%. Broadband data keep their tuned 3 sigma clip unchanged. The trim stays reachable with --background-trim for back compatibility; setting either estimator clears the other, so they can never stack. --integrator boxsum does not take the clip (matching what the shipped clip already did), so it now uses the plain ring mean unless --background-trim is given. The intensities get measurably more accurate: per-shell agreement with an independent processing of the same images improves on 14 of 16 crystals (weighted -0.0347, outermost shell 12/4), the outermost-shell R_meas NUMERATOR - absolute scatter, not a denominator effect - falls 13.5% median on 16/5, and CC1/2 in the outer shell improves on 14/7. EXPECT <I/sigma> TO FALL AND EDGE R_meas TO RISE. Both are inflated by information-free counts, so both get worse when the bias is removed; neither is evidence against this change. That fingerprint is exactly how the trimmed mean was accepted in the first place. Known cost: over the 37-crystal rotation battery the de-novo space-group count goes 34 OK / 3 DIFF to 33 / 4. The single regression is a two-lattice crystal whose merge fails the absolute-sanity gate under either background (R_meas 63.5%, CC1/2 72.2%) and which carries an unresolved indexing ambiguity on the very operator being scored, so its operator CC is diluted by construction. No other crystal changes space group, and twin protection is not weakened - the H-ratio veto that refuses genuinely twinned crystals gets MORE decisive (1.63 -> 1.84, 2.83 -> 3.99). Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-05 18:03:11 +02:00
leonarski_fandClaude Opus 5	fb55645b81	Revert "rugnux: fit the profile radius from the strongest spots too" ... Reverts the profile-radius part of 457b1bfd1; the comparison-script and mosaicity-column changes from that commit are kept. The cap was validated on the rotation battery, which cannot test it: the profile radius feeds `ewald_dist_cutoff` in IndexAndRefine, and that is read only by the STILLS predictors (BraggPrediction/BraggPredictionGPU). The rotation predictors gate on the mosaicity window instead and never look at it. So "no space-group changes, 36 of 37 crystals bit-identical" showed the quantity is inert for rotation, not that capping it is safe - and the one regime where it does act was never exercised. Validating it needs the serial-stills battery, which is a much larger exercise. Until then the arbitrary constant is not worth carrying in a code path nobody measured. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-04 21:35:17 +02:00
leonarski_fandClaude Opus 5	5eb386e333	docs: describe the per-frame geometry smoothing ... Goes in §10.3 next to the per-frame scale and mosaicity smoothing, since it is the same mechanism applied for the same reason, and trims the changelog line to one sentence. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-04 20:23:19 +02:00
leonarski_fandClaude Opus 5	017f64690c	rugnux: smooth the per-frame geometry before scaling ... Geometry is re-refined independently on every frame, against that frame's spots alone - as few as a dozen on a sparse crystal, where XDS fits its equivalent to about sixty times more data. Measured over ten datasets the per-frame orientation carries two components: a slow drift that is real, with rugnux and XDS agreeing to R^2 0.83-0.88 on the two crystals that genuinely slip by 1.5 and 0.54 degrees, and a fast jitter that is fit noise, scaling with spots-per-frame at exponent -0.79 where counting noise alone would give -0.5. The jitter is worth 1-8% on merged intensities, 24% on the sparsest crystal. It cannot be fixed by refining less. Turning per-image refinement off entirely loses six space groups and a whole crystal, and even a 624-spot-per-frame crystal collapses; dropping the beam-centre terms holds the space groups but is worse on 31 of 37 crystals. The freedom is earning its keep, so keep it and suppress only the band that cannot be physical - a crystal does not re-orient and snap back from one frame to the next. So smooth the orientation in frame order after integration and recompute each partial's delta_phi, and hence its partiality, from the smoothed lattice. Batching at integration time was not an option: frames are processed independently and the online path depends on that. This runs before the GPU upload, so the device path picks it up with no separate kernel. The window is chosen per dataset by leave-one-out cross-validation, because the two components vary far too much for one number - drift spans 0.018 to 1.288 degrees and jitter 0.005 to 0.221, so any fixed window over-smooths one crystal while under-smoothing another. Chosen windows range from +-1 to +-20 frames. It is capped: cross-validation scores how well neighbours predict a frame's orientation, which on a barely-drifting crystal keeps improving with width, but the per-frame fit is also absorbing a real per-frame systematic and smoothing too wide destroys it - uncapped, one crystal chose +-60 and lost 16% of its ISa. Battery over 37 crystals: space groups unchanged at 34 matching XDS, R_meas better on 31 and worse on 6, low-resolution R_meas 30/7, ISa 26/10, high-resolution CC1/2 23/12. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-04 20:06:41 +02:00
leonarski_fandClaude Opus 5	457b1bfd1d	rugnux: fit the profile radius from the strongest spots too ... Same defect as the mosaicity in 2c94f3013, in the same file's sibling fit. The profile radius is an RMS of the excitation error over whatever spots were kept, and weaker spots sit further off the Ewald sphere, so it grows with the depth of the list: measured over a 150 -> unlimited spot budget it rises ~60%, and on a clean dataset as much as on a hard one, so this is general rather than something one awkward crystal provoked. That made it a function of --max-spots, which is an indexing budget, rather than of the crystal. Its one consumer treats it as a membership gate (ewald_dist_cutoff is twice it) where reflections at the cutoff carry near-zero partiality and are removed downstream anyway, so the integrated data barely notices: with the mosaicity already pinned, the partial count moves 0.2% across a 34% change in the radius. It is also reported per image as a diagnostic, though, and a number that slides with an unrelated setting is misleading to anyone comparing two runs - and it would stop being benign the moment anything used it as a width rather than a gate. Battery over 37 crystals: no space group changes, 36 of 37 bit-identical, no failures, one crystal marginally better. Also in the comparison script: report XDS's mosaicity next to rugnux's. XDS has two and they are not interchangeable - CORRECT.LP's REFLECTING_RANGE_E.S.D. is post-refined, while INTEGRATE.LP's per-batch SIGMAR is its integration-stage estimate, and the two differ by up to 2.3x. The XDS cell now prints both as postrefined|MLE so a per-image estimate is compared against the one measured the same way. Fixes a scoping bug in the same addition where every crystal read the last directory's INTEGRATE.LP. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-04 10:52:30 +02:00
leonarski_fandClaude Opus 5	2c94f3013e	rugnux: fit the mosaicity from the strongest spots only ... The per-image mosaicity MLE ran over the whole indexed spot list, so it rode on --max-spots, which is an indexing budget. A spot is detected when I_full * R(tau) clears the finder threshold, so selecting by intensity censors on R(tau): a deeper list holds proportionally more large-|tau| partially recorded spots and the fit widens with it. Raising the budget 250 -> 1000 widened sigma_M 0.059 -> 0.075 deg on a rotation dataset whose measured rocking width says 0.054. That is not cosmetic. An over-wide mosaicity mis-states every partiality in scaling: forcing the mosaicity across that range moved the merge error model from b 0.039 / ISa 26 to b 0.167 / ISa 6, and the space-group search lost a genuine 422 with it, merging the crystal in 222 instead. Cap the fit at the strongest 250 spots. FilterSpotsByCount leaves the list strongest-first, so this selects exactly the spots a smaller --max-spots would, and the mosaicity becomes invariant: 0.0538 deg at 250, 500, 1000 and 2000 spots, with the correct space group at each. Trimming or down-weighting the tau tail does not work - the censoring is multiplicative in R(tau), so it widens the whole distribution rather than adding a tail. Battery over 37 crystals: exactly one change, the demoted crystal repaired (33 space groups matching XDS -> 34). 23 of 37 are bit-identical, never reaching 250 spots. Unaffected elsewhere: the default spot count is 250, and stills have no goniometer so they return before the fit. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-04 07:34:40 +02:00
leonarski_fandClaude Opus 5	cd0c43c65c	docs: add the packaging and documentation work to the rc.161 change list ... Covers the Debian package rename and the DKMS scripts, the writer's --verbose, the version plumbing, and the documentation pass - the release-contents page, the corrected repository URLs and package names, and the rugnux, viewer and writer pages. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-03 20:53:48 +02:00
leonarski_fandClaude Opus 5	ceb92fc4cc	docs: bring the rc.161 change list up to date ... Covers the GPU decode work (fused un-transpose, the memory it frees, corrupt-chunk detection, large bitshuffle blocks, host fallback), the two reproducibility fixes (integer ring statistics, striped geometry-refinement sampling), the connection-teardown and written-extent fixes, and the thread-count, max_hkl and compression-time repairs. Folded into the existing entries where they belong rather than added as new ones. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-03 16:58:03 +02:00
leonarski_fandClaude Opus 5	b6c4a59d69	docs: record the stored-format break, and say how the adaptive finders actually accumulate ... The per-image image-scale B factor was dropped from the CBOR stream and from the written HDF5, which is a change for anything reading those files, but the changelog listed it only under the OpenAPI breaking changes. The GPU adaptive finder test claimed both finders sum the rings in double. The CPU one does; the GPU one stages a block's contribution in float before reducing across blocks in double, deliberately, to keep the hot loop's shared footprint down. Say so, and say what follows from it - detection compares integer pixel values, so a threshold that crosses an integer flips every pixel of that value in the ring at once. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-03 14:14:24 +02:00
leonarski_fandClaude Opus 5	47277674fa	docs: split the breaking API changes out of the rc.161 change list ... Earlier releases put breaking changes in their own paragraph after the bullets (rc.139, rc.29) rather than as one item among them. Follow that: the OpenAPI changes now sit under their own heading below the list, with the client-side action in the lead line, and are listed one per change instead of run together. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-03 07:46:57 +02:00
leonarski_fandClaude Opus 5	737cbde3ff	docs: tighten the changelog and the decoding section for release ... The rc.161 changelog had grown entries several hundred words long and listed the same area three or four times over. Collapse them by subject - spot finding, resolution limits, space-group search, scaling, performance, correctness - and hold each to one line, keeping the actionable detail in the breaking API entry. Add the performance work that had not been written up: device-side image decoding and the parallel first-pass candidate-cell refinement. Section 0 of the CPU analysis document was the longest thing in it after two core algorithm sections, and most of that was a profiling narrative and the measurements that motivated the change rather than a description of what runs. Cut it to the two kernels, the host-side block scan and the fallback rule. The attribution stays; it is also in the reference list. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-03 07:44:55 +02:00
leonarski_fandClaude Opus 5	0ca159449f	Bragg integration: integrate as far as the detector reaches, not to a fixed 1.0 A ... BraggIntegrationSettings::DMinLimit_A had a setter that nothing anywhere called, so it was always its 1.0 A default - in rugnux, the viewer and the broker alike, with no option or API field to change it. It feeds the predictor as high_res_A, which discards any reflection with |q| > 1/d_min, so integration simply stopped at 1.0 A however far the detector reached. Five of the 33 rotation test datasets have detectors reaching past it, down to 0.981 A. On one of them, run with no resolution limit, the shell table ended dead at 1.00 A with that shell still at CC1/2 55.6% and <I/sig> 3.4 - cut mid-shell rather than fading out. This branch had already made the sibling limits detector-driven (spot finding, scaling), so the pipeline was finding spots the detector could see and then refusing to integrate them. Make it a std::optional: unset means as far as the detector reaches, a value limits. The limit is only a bound on how far the lattice walk goes, never a second opinion on what is measurable - both predictors independently drop reflections that miss the detector (BraggPrediction.cpp, BraggPredictionRot.cpp) - which is what makes the detector's own reach the right default. rugnux gains --integration-high-resolution (0 = no limit, as for --spot-high-resolution); the derived per-axis prediction range resolves against the same number, so the two cannot drift. Full battery: 30/33 space groups, unchanged from before, 0 failures and the same three known mismatches; 22 of 32 crystals bit-identical and nothing worse than 5 observations in ~500k. The datasets that gain do so because their detector reached past 1.0 A - the effect is understated here because the harness caps each merge at the XDS resolution anyway. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-31 14:03:34 +02:00
leonarski_fandClaude Opus 5	b0e315e73c	Bragg prediction: derive the lattice walk from the cell, and expose it in the API ... Follow-up to making max_hkl a setting: it is now an optional, and unset means "take it from this crystal". The predictor keeps only |q| <= 1/d_min and h = a.q for the real-space axis a, so |h| <= a/d_min exactly - and likewise |k| <= b/d_min and |l| <= c/d_min. max(a,b,c)/d_min therefore bounds all three at once: nothing that could be predicted lies outside it, and nothing inside it is reached by a shorter axis. It applies to rotation and stills alike, both going through the one place the prediction settings are built. Offline (rugnux, viewer) the default is unset, so every crystal gets its own range; --max-hkl overrides it. Online the broker holds a concrete number, because the cost is the cube of it per image and a live acquisition should not have its frame rate decided by whichever sample is mounted: max_hkl joins bragg_integration_settings in the OpenAPI with a default of 100, so an omitted field arrives as that default (the generated model carries it) rather than as "derive it", and the frontend exposes it next to the integration model. Measured against a fixed 100 on six rotation crystals: three are bit-identical, two were being truncated and recover 419k and 5.8k observations with the high-shell CC1/2 going 15.1 -> 25.8% and 52.1 -> 55.3%, and the space group is unchanged 6/6. It reproduces a fixed 200 exactly, which is the bound being tight rather than merely safe. The sixth is worth recording: a 149/83/226 A cell derives 227, and because a single scalar has to cover the longest axis the cube is ~16x what a per-axis box would be - 22% wall clock, for a net 22 observations out of 364k (the per-frame 65536-reflection cap re-selects at the margin when more candidates are offered) and identical CC1/2, ISa and space group. Per-axis limits would remove that; the predictors already map a thread index to h, k and l separately. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-31 13:10:58 +02:00
leonarski_fandClaude Opus 5	a06c06931f	Bragg prediction: how far to walk the lattice is a setting, not a literal ... max_hkl was hardcoded to 100 at the one place production builds the prediction settings, so the only way to change it was to edit and rebuild - and it is not a constant of the method, it is a property of the cell. An axis is truncated once a/d_min exceeds it: 100 covers a 150 A axis at 1.5 A, but the same axis at 1.0 A, or a 250 A axis anywhere, loses its outermost reflections with nothing said. Move it into BraggIntegrationSettings next to the other prediction/integration parameters and add rugnux --max-hkl (1..511, default 100 - no behaviour change). Like the integration radii and the background trim it stays out of the OpenAPI, so the broker keeps the default it has today and live analysis cannot be handed a range that would not finish; the offline front end, which knows its cell, can ask for more. RugnuxCommandLine emits it when it is not the default. Measured on five rotation crystals at --max-hkl 200: two are bit-identical at no cost, and three were being truncated - one gains 419k observations (+17%) and takes its high-shell CC1/2 from 15.1% to 25.8% for +14% wall clock, the other two gain 12k and 5.8k observations with CC1/2 76.6->82.4% and 52.1->55.3% for +9% and +1%. ISa is unchanged throughout, and no frame overflowed the prediction buffer. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-31 12:00:45 +02:00
leonarski_fandClaude Opus 5	3e56d96921	Stills partiality: adopt the refined tilt only when it fits better ... RefineOne re-measured the image's correlation to the reference after writing the refined partialities - because --min-image-cc drops images by it - and then ignored what it measured. A crystal the tilt model suits worse than the fixed partiality it replaces kept the refined model anyway, and the refinement is on by default. Compare against the CC the crystal arrived with and put it back untouched when the refinement does not improve it, which is the same state a crystal with too few reflections to fit ends in. Also four things noted in review and left until now: AdaptiveThresholdTest.cpp was listed twice in the test target, AdaptiveThreshold.h was the one header in image_analysis/spot_finding not in its library's source list, CLAUDE.md said update_version.sh rewrites VERSION when it only reads it, and the CHANGELOG did not mention that image_scale_b is gone from the plot_type enum - which breaks a client that asks for that plot. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 22:03:18 +02:00
leonarski_fandClaude Opus 5	a770f0857b	CHANGELOG: record the rc.161 fixes ... Also corrects the reader bit-depth entry: taking the depth from the file was the wrong fix for the 32-bit EIGER2 case and broke 8-bit files. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 11:42:04 +02:00
leonarski_fandClaude Opus 5	0f1851cf82	rugnux: drop the 1.5 A spot-finding limit on rotation data ... Rotation kept a 1.5 A high-resolution limit for spot finding on the strength of one indexing-rate measurement (100.0 -> 96.8% on a strong set). Measured properly, over the whole 33-crystal rotation battery, it does not earn its place: * no space-group decision changes - the same 30/33 agree with XDS, and the three that differ are the known pre-existing cases, unchanged; * 29 of 33 crystals are identical to the digit - same indexing rate, R_meas, CC1/2, ISa. The limit was doing nothing on the large majority; * where it does bite, the limit is the worse setting. The one crystal that loses appreciable indexing rate without it (99.50 -> 94.22%) comes back with lower R_meas (29.4 -> 28.1), higher high-resolution CC1/2 (27.9 -> 29.1) and higher ISa (5.77 -> 6.17). Another loses 0.4% of frames and gains 2.8 points of CC1/2_hi. Fewer frames indexed, better data from them; * runtime is unchanged (16m46s vs 17m32s over the battery). So the indexing-rate cost is real but does not carry through to the merged data, which is what the limit was protecting. Unset now means "as far as the detector reaches" for rotation as well as stills; --spot-high-resolution still sets a limit for weak, high-background data where the extra high-resolution spots are genuinely noise. This also removes the flag that distinguished "the user asked for no limit" from "the user said nothing" - with no rotation default left, both mean the same thing. While rewriting the comment block, corrects its neighbouring claim that rotation keeps the fixed-threshold finder; adaptive detection has been the default for both workflows since 6f4917dce. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-29 10:39:23 +02:00
leonarski_fandClaude Opus 5	648e8c62c8	CHANGELOG: record the two settings fields that are no longer required ... Making azim_int_settings.high_q_recipA and spot_finding_settings.high_resolution_limit optional changes the wire format: when unset they are omitted rather than sent with a placeholder, and a client generated from an older spec does j.at() on them. The azimuthal-integration limit now defaults to unset, so a stock broker omits it out of the box - the break needs no operator action to hit. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-29 09:38:38 +02:00
leonarski_fandClaude Opus 5	40acf1ffc4	rugnux: search the space group twice by default on rotation data ... --search-min-zeta now defaults to 0.85 for rotation, so the de-novo search runs on a merge of all the observations AND on a merge of only the well-measured ones, and keeps whichever found more symmetry. Previously it shipped off and the second opinion had to be asked for. Rotation battery, 33 crystals, NO flags beyond the resolution limit: fixed-threshold finder 30/33 - zero crystals differ from the single search adaptive finder 30/33 - the same three mismatches Both arms now agree crystal for crystal, which they have not done before. The last disagreement was a thaumatin set whose 4-fold sits 88.9 deg from the spindle: at defaults it now reads P42(1)2 (all-observation merge -> 222, Lorentz-filtered -> 422, higher taken) where it read P222. The classic arm is a strict no-op - zero differences against both the explicitly-flagged run and the run predating the dual search - so the default costs nothing where the geometry is not the problem, and 47.2 s against 47.8 s on the same crystal back to back. The default is safe to set because the two searches can only disagree by a LOST operator: discarding observations starves an operator correlation, it cannot invent one. That also makes the 0.85 itself uncritical - too aggressive a cut only means the second opinion contributes nothing and the full merge wins. --search-min-zeta 0 restores the single search. Docs: CHANGELOG gains a 1.0.0-rc.161 section covering the branch, and CPU_DATA_ANALYSIS records the four analysis changes of this work - the confidence-weighted per-image refinement, the collapsed per-frame scale guard, the opt-in per-image rejection, and the operator-disagreement criterion with the two-search rule. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-28 21:56:36 +02:00
leonarski_f	67dca388bd	v1.0.0-rc.160 (#70) ... 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. * rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #70 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-19 09:39:28 +02:00
leonarski_f	dd0bffb283	v1.0.0-rc.159 (#69) ... 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. * rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #69 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-13 13:54:03 +02:00
leonarski_f	451310f43d	v1.0.0-rc.158 (#68) ... 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. * Analysis: The azimuthal-integration solid-angle correction now follows the incidence angle to the detector normal (`cos^3` of that angle) instead of `cos^3(2*theta)`, so it is correct for a tilted detector and matches PyFAI `solidAngleArray` and MAX IV azint (unchanged for an untilted detector). Crystal geometry refinement (`XtalOptimizer`) no longer silently ignores an imported PONI `rot3` (rotation about the beam): it is applied as a fixed rotation in the residual so refinement stays consistent with the rest of the pipeline. Polarization and azimuthal binning already honoured `rot3` through the full PONI rotation. * jfjoch_viewer: Open datasets on the WSL2/UNC filesystem (paths starting `\\`); write processing outputs next to the input file, with a Browse button and independent `_process.h5` / merged `.mtz`/`.cif` toggles; and show the determined space group in the merge-statistics window. * rugnux: Accept an absolute `-o` output prefix in offline processing. * Packaging: The self-contained Linux viewer `.tgz` now bundles cuFFT, so it runs without a system CUDA toolkit (`.deb`/`.rpm` are unchanged, distro-managed). * Docs: Bring the analysis references up to date with the code. `docs/CPU_DATA_ANALYSIS.md` now reflects the unified profile-fit Bragg integration engine, multi-lattice indexing, azimuthal phi binning, the radial parallax/bandwidth profile with sub-pixel centring, the rot3d capture-fraction handling and the automatic CC1/2 resolution cutoff, and drops the descriptions of features that were never implemented (French-Wilson amplitudes, the still excitation-error partiality model); `docs/RUGNUX.md` documents the new `--resolution-cutoff`/`--resolution-cc-target`/`--resolution-shells`, `--min-captured-fraction`, `--mosaicity`, `--reference-column`, the azimuthal correction toggles and the geometry-override options, and corrects the `-N` default. The outdated in-source design notes (ICE_RING_DETECTION, BRAGG_INTEGRATION_ENGINE, NEXTGEN_INTEGRATOR) are removed.Reviewed-on: #68 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-12 19:42:29 +02:00
leonarski_f	54c0100e8e	v1.0.0-rc.157 (#67) ... 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. * rugnux: Rebrand the offline data-processing subsystem as `rugnux` and consolidate all offline analysis into the single `rugnux` binary - `jfjoch_process` is now `rugnux`, the former `jfjoch_azint` is now `rugnux --azint-only`, and `jfjoch_scale` is now `rugnux --scale` (see the new docs/NAMING.md and docs/RUGNUX.md). Scaling and merging are on by default for rotation and stills (`--no-merge` disables them), replacing the previous opt-in `-M, --scale-merge`. * rugnux: CLI fixes - default `-N` to all hardware threads, parse numeric option arguments strictly (reject non-numeric or trailing input instead of silently yielding 0), require `--wavelength > 0`, and correct the reproduced command line and `--scale` reference-cell handling. * rugnux: De-novo space-group improvements - recover genuine high symmetry and centred Bravais lattices from intensities, add an automatic CC1/2 high-resolution cutoff, and report L-test twinning statistics. * rugnux: Index weakly-diffracting low-resolution rotation data that previously failed (e.g. F-cubic crystals that diffract only to ~4 A on a detector reaching ~1.5 A). The per-frame indexing gate now measures the indexed fraction only within the resolution range the lattice actually diffracts to, so the many sub-diffraction ice/noise spots no longer make the fraction floor unreachable; the two-pass first pass tries several image-sampling schemes (spread across the whole rotation vs a consecutive wedge whose native stride keeps a reflection's rocking curve continuous, letting the FFT resolve a long axis) and keeps the one that indexes the most frames; and the de-novo space-group search no longer discards all reflections (and crashes) when every resolution shell falls below <I/sigma> = 1. * rugnux: Lower the low-resolution R-meas for strongly-diffracting rotation data - drop edge-of-sweep truncated fulls whose rocking curve was captured below `--min-captured-fraction` (default 0.7 for rotation), and report R-meas only over the observations kept by outlier rejection (matching XDS). The 0.7 default also strips the partiality-extrapolated fulls that dominate the intensity second moment on weakly-diffracting crystals, so the de-novo space-group search is no longer starved by the error-model I/sigma floor and recovers the correct symmetry (e.g. the F-cubic Benas crystals: Benas_3 -> F432, Benas_7 -> P6122, instead of P4/P1); on the reference battery every other crystal keeps its space group. * rugnux: Write the refined geometry (beam, tilt, axis) to _process.h5 and place non-standard mmCIF items under a reserved `jfjoch` prefix. * jfjoch_broker: Ordinary acquisition failures (receiver/writer/analysis problems, missed packets, writer disconnect) now return to the Idle state with an Error-severity message, so a run can be retried without an expensive re-initialisation; only failures that leave the detector in an undefined state (new JFJochCriticalException, e.g. PCIe/FPGA faults) go to the Error state and force re-initialisation. * jfjoch_broker: A synchronous /start now reports its failure to the HTTP caller instead of returning HTTP 200, and an incomplete or truncated dataset (missing packets, writer disconnect) is reported as an error rather than a "reduce frame rate" warning. * jfjoch_broker: Drop uncollected placeholder rows (number = -1) from the scan_result REST endpoint. * jfjoch_broker: Fix the inverted per-image compression ratio reported by the Lite receiver (was compressed/uncompressed instead of uncompressed/compressed). * jfjoch_broker: Bragg integration adds a quantization-noise variance floor with a box-sum fallback, and treats the type-maximum marker as an invalid pixel for unsigned image types. * jfjoch_writer: Detect file-overwrite conflicts at start for back-channel transports, and reset the writer when end-of-collection finalisation fails. * jfjoch_viewer: Preview overlays follow the geometry (resolution/ROI arcs, true beam centre, predictions, coral secondary-lattice spots, legend), add save-as-JPEG, and fix an HTTP live-follow memory leak. * Frontend: Improved aesthetics and usability, and added in-browser pixel-mask and JUNGFRAU-pedestal visualisation. * CI: Name the Windows installer jfjoch-viewer-* instead of jfjoch-*.Reviewed-on: #67 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-11 07:19:11 +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	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	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>	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	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	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>	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	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	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	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	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	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	2ab9deb20b	v1.0.0-rc.123 (#40) ... Documentation update Reviewed-on: #40	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	2026-03-07 11:34:04 +01:00