18 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	b5f5879a1d	rugnux: measure the ice in the first pass, and always find its own spots ... Ice handling was gated on a measurement the run only made AFTER the images had been processed, so the per-image pass could not use it. The flagging therefore ran unconditionally: ice-band spots were ordered last in the --max-spots budget and held out of the indexer seed and the geometry refinement on every crystal, iced or not. The eleven bands are fixed geometry holding 16-26 % of the unique reflections whether or not there is ice, so on a clean crystal that discards a fifth of the spots - the strongest first - for nothing. Measured on a crystal whose gate never fires, that moved the merged data by a mean of 0.85 sigma against a run-to-run floor of 9.3e-5. Measure it in the first pass instead. That pass already looks at ~100 images spread over the sweep, and it already stops at the spot finder, so it sees the azimuthal profile for the smooth channel and the unfiltered connected components for the spot channel. Both counts SpotAnalyze takes are pre-filter, so pooling them there is the run's own verdict, reached before anything has been discarded and in time for the pass that acts on it. Where the sample sees no ice, the run indexes on the ice-band spots too. It has to be the whole sample: the spot channel is a ratio pooled over images, because one frame carries a handful of control spots. A per-image gate is not an alternative - two of the crystals whose indexing this rescues fire on that channel alone, at profile scores of 1.12 and 1.22, so gating per image on the profile score would drop exactly the cases that matter. This also removes the first-pass spot reuse, and with it --redo-rotation-spots and the reuse path. Finding the ~100 first-pass spots costs little, and reusing was actively wrong here: the stored spots were found online at the acquisition's threshold and have already had their ice-band entries ordered last and dropped by its spot budget, so counting ice from them under-reads it by construction, and the lattice search never saw the spot-finding settings at all. It also removes the need for the machinery that re-found spots whenever a spot-finding option was named, which made those options impossible to A/B. IndexAndRefine cached index_ice_rings at construction, which happens before the first pass; it holds a reference to the experiment, so it now reads the setting where it uses it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-06 20:48:22 +02:00
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	61a7c91b90	Ice: detect it on two channels, and only handle it when it is there ... The per-image ice score was read off the PLAIN azimuthal profile. That profile is a per-ring mean, so a few strong Bragg reflections landing in a ring's q bin lift it exactly as ice would. Measured over 37 rotation crystals, that did not merely add noise - it INVERTED the metric: the two highest-scoring crystals had no ice at all (4.23 and 4.06), while a clean control read 1.57. A decoy null - the identical statistic evaluated at q positions where hexagonal ice cannot be - reaches 1.51 at its 99th percentile and 2.70 at its maximum, so that metric cannot support any absolute threshold whatsoever. The adaptive spot finder already computes the right input for its own threshold: a sigma-clipped per-resolution-ring background, in the same bins. A powder ring is azimuthally smooth and survives the clip; Bragg peaks do not. On the clipped profile the clean population tightens to 1.00-1.22 and the crystals with confirmed ice sit at 2.08-2.37, against a decoy null that never exceeds 1.29. That channel is blind to one thing: ice in large crystallites diffracts as DISCRETE spots and leaves the radial profile flat. So a second channel counts found spots on the rings against the same q width of ice-free flanks beside them. The two barely overlap - the smooth-ice crystals read 2.1-2.4 / ~1.0 and the textured ones ~1.1 / 3.8-17.6, while a clean crystal reads 1.04 on both. Both are then used as a GATE (--ice-min-score 1.5, --ice-min-spot-ratio 2.0, both calibrated on the battery, 0 disables): the eleven fixed hexagonal bands cover 16-26 % of the unique reflections at typical resolutions whether or not the crystal has ice, so flagging, the exclusion from the scale fit and the merge-time CC1/2 ring mask are now all skipped when neither channel sees any. The gate is applied in the full pipeline and in --scale, which reads the stored per-image values back out of the _process.h5. Also fixes the merge-time mask's control: the shoulder now excludes reflections that are themselves on an ice ring. The rings are not evenly spaced - 1.947/1.916/1.882 A sit 0.05-0.06 apart in q - so for those three the [w,3w) shoulder landed squarely on the neighbours and the test compared ice against ice. Measured, that is the only thing this changes: it removes firings on those three rings and leaves every other firing's CC pair identical to three decimals. And the online ice half-width, which was 0.02 in the API against 0.03 offline, so the same data got a narrower band online than the measured ~0.06 ring FWHM justifies. Battery (37 rotation crystals, against the previous behaviour): space groups 34/37 in both and NO crystal's space group changes; 6 crystals gain unique reflections, 1 loses. Best of them gains 7082 unique reflections with R_meas 16.0 -> 14.3, CC1/2 95.9 -> 97.3 and ISa 13.7 -> 19.0; another goes R_meas 54.9 -> 42.9, CC1/2 84.0 -> 90.4, ISa 3.9 -> 5.5; a third reaches CC1/2 99.4 from 95.7 at an unchanged reflection count. The one crystal that loses reflections improves on both R_meas and CC1/2. Not done here: the ScanResult/API/plot-type/frontend/viewer layers for the new spot_count_ice_control (they need the OpenAPI regeneration). Message, CBOR, HDF5 write/read and the receiver plots are. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-06 16:17:23 +02:00
leonarski_fandClaude Opus 5	bb7df09086	rugnux: separate the merge-time ice-ring mask from ice detection ... --detect-ice-rings did two unrelated jobs at once: flagging ice spots so indexing de-prioritises them and keeping ice reflections out of the scale fit, AND gating the merge-time mask that drops a decorrelated ice ring and re-merges. Turning it off to de-confound a merge-stage experiment therefore also changed how the data were indexed - measured, that breaks indexing outright on two of the 37 rotation battery crystals - while leaving it on lets the mask land differently between two arms of an experiment and contaminate the comparison (measured on up to 19 of 37 crystals in response to a small intensity change). Add --ice-ring-mask[=on|off], default on, gating only the merge-time mask. Verified with =off: ice-spot flagging and the scaling exclusion still log and still apply, no mask line, no second merge, and the first error model is bit-identical to the =on arm. The full pipeline and the offline --scale path reach the same verdict on the same data, as they must. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-05 19:00:10 +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	f25fea7024	rugnux: keep 1000 spots per image instead of 250 ... Offline reprocessing is not bound by the online spot budget, and the cap is applied at the end of SpotAnalyze, so it is exactly the spot list the indexer and the per-image refinement see. jfjoch_viewer already sends 1000, so the two front ends now agree on the same file. Measured as a paired A/B over the 37-crystal rotation battery, de novo, with the resolution and Friedel setting matched to the XDS reference, both arms from the same binary bar this constant: R_meas low shell 16 better 0 worse 19 unchanged R_meas 14 better 4 worse 17 unchanged ISa 14 better 6 worse 15 unchanged CC1/2 6 better 3 worse 26 unchanged Low-resolution R_meas is a clean sweep. Around half the battery is bit-identical: those frames never reach 250 spots, so the cap never bound. Wall clock is unchanged (10m00s vs 10m44s, uncontrolled for page cache). Known cost, and the reason this is its own commit: one crystal in the battery reproducibly loses symmetry, tetragonal 422 -> orthorhombic 222, doubling its asymmetric unit. Its R_meas and ISa "improve" there, but that is what merging in too low a symmetry always does, and the lower symmetry then admits a merohedral indexing ambiguity. An intermediate cap of 500 demotes it too, so it buys none of the safety. This is the known point-group-decision-moves-with-data-amount fragility of the space-group search rather than an argument for starving the indexer of spots - the search is the thing to fix. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-03 22:08:21 +02:00
leonarski_fandClaude Opus 5	2473e03cf7	rugnux: default --spot-sigma to 4.0, the value the viewer already uses ... The two front ends disagreed on the fixed-threshold spot finder: rugnux started from 3.0, jfjoch_viewer from the SpotFindingSettings default of 4.0, so the same file processed either way could give different spots. Inert on the default path - the adaptive finder derives its threshold from each image's own per-resolution-ring noise and never reads signal_to_noise_threshold (only ImageSpotFinderCPU/GPU and DetModuleSpotFinder do). It changes behaviour only under --no-adaptive-spots, and there it now matches the viewer. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-03 22:07:58 +02:00
leonarski_fandClaude Opus 5	cfcb84aece	docs: bring the tool pages back in line with the programs ... rugnux gained --model - R-free and 2Fo-Fc/Fo-Fc maps against an atomic model, and with it the resolution of the enantiomorph and of a merohedral indexing ambiguity - without the page ever mentioning it. It was the only option missing; the two lists now agree in both directions, checked against the usage the binary prints. The viewer page still said results are never saved and that no Windows package exists. Both have been false for a while: the Processing panel runs full rugnux jobs on the open dataset, writes _process.h5 and the merged reflections, registers each run as a selectable view so runs can be compared, and can hand out the equivalent command line for a cluster; and the installer is published with every release. The mask menu also loads TIFFs now, and the View menu has layout presets. The writer page documented -R for the root directory, which is the back-compatibility alias for -d, and an HTTP status interface that no longer exists - status reaches the broker over the writer notification socket, and a writer is stopped with a signal. The test page pointed at .gitlab-ci.yml and at jfjoch_offline_process, which is not a binary any more; the CrystFEL fixture pointed at HDF5DatasetWriteTest, which is not either. The broker page linked ../broker/redoc-static.html, which MyST resolved by copying the 700 kB file into _downloads/ rather than using the copy already in _static. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-03 20:53:37 +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	3b9e1424ea	docs: RUGNUX.md on adaptive detection and --search-min-zeta ... Adaptive spot detection became the default for rotation data as well in 6f4917dce; RUGNUX.md still said rotation kept the fixed-threshold finder, which is also the opposite of what the usage message and CPU_DATA_ANALYSIS say. --search-min-zeta had no entry in the option tables at all. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 11:23:11 +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	16bf3408f0	Address code-review findings; make detection limits detector-driven ... One changeset, developed together in response to a review of this branch, so the files carry several of the changes at once. Full test suite passes (733 cases). Spot finding - Split ImageSpotFinder into Detect() (flag strong pixels - the expensive per-pixel pass) and ExtractSpots() (CCL + min/max-pix + resolution mask), with Run() = both. The per-image min-pix escalation now detects ONCE and repeats only the cheap extraction, instead of re-running the whole finder four times per frame as it did on the default path. It also keeps the winning attempt's spot list rather than re-extracting it, so the frame that is integrated is exactly the frame that was scored - which a GPU re-extract could not guarantee (float atomic ordering). - spot_finding_time_s no longer swallows indexing time, and indexing_time_s now sums every escalation call instead of reporting only the last. Detection limits follow the detector - The azimuthal-integration upper q and the spot-finding high-resolution limit are now std::optional, in the C++ structs AND in the OpenAPI schema, and resolve to the detector's own maximum (DiffractionExperiment::GetDetectorMaxQ_ recipA). Adaptive detection reads a pixel's ring from the azimuthal bins, so a pixel outside that q range could never be strong - the integration range silently bounded what detection could see, regardless of the requested resolution limit. Regenerated the C++ and TypeScript clients; the viewer and the web frontend each gained a "to detector edge" switch. Detection defaults are now per workflow (measured, not assumed) - Stills: adaptive detection, min-pix chosen per image, no resolution clipping. - Rotation: fixed-threshold finder, min-pix 2, 1.5 A limit. On a 33-crystal rotation battery, adaptive detection helped four hard crystals but deterministically broke three (a lost space group, a halved indexing rate, a collapsed merge), and the detector-edge limit cost indexing on a strong rotation set (100.0 -> 96.8%). Each is still overridable by its flag, and --no-adaptive-spots is new. Indexer seed escalation - Stop escalating once a seed's lattice explains >= 90% of the seed spots. Previously any frame with >= 80 spots always paid three indexer calls, online broker included. Merge-consistency filter - --min-image-cc gated on a per-image CC computed BEFORE the stills partiality post-refinement and never refreshed; the refiner now recomputes it, so the reported CC describes the data that are actually merged. - Replaced the per-call cc_mask argument with one MergeOnTheFly flag, so the merge, the error model and MergeStats can no longer disagree about which images are in (the --scale path merged unfiltered while its statistics were filtered). Per-image B-factor refinement (-B) removed - Measured on four serial-stills datasets: it is a no-op where the per-image fit is well conditioned and actively harmful where it is not (CC1/2 -8.1, R_meas +23.2 on the weakest large-cell set, whose fits hit their [-50, 200] bounds on 14-25% of images). It had also been silently DISCARDED since the partiality post-refinement landed - reported but not applied. Rather than fix and keep a knob with no demonstrated benefit, the flag and the whole image_scale_b_factor chain are gone: setting, scaling fit, message field, CBOR, HDF5 write and read-back, per-image plot, OpenAPI enum, viewer column and checkbox, docs. ScaleOnTheFly no longer needs Ceres at all - the fit is a linear IRLS. (The Wilson per-image b_factor is a different quantity and stays.) Stills partiality width now fits both of its components - sigma^2 = gamma0^2 + (gamma_e*d*)^2 instead of a purely angular gamma_e*d* with gamma0 pinned to 0. Fitted per crystal by least squares of dist_ewald^2 on d*^2. The angular-only width is fitted over a d*^2-dense population, so it was pinned by the high-resolution edge and collapsed at low d*: median partiality 0.008 beyond 13 A for reflections that were plainly recorded, 55% of them under the merge's partiality floor, and the survivors divided by those values - which inflated the merged low-resolution intensity scale 3.6x (~ +9 A^2 of apparent B). Measured on 5000 stills: the ramp flattens to 0.89x, no observation is dropped any more (701750 -> 716811), shell-mean CC1/2 and R-free improve slightly. Note CC1/2, R_meas, completeness and a B-refining R-free are all blind to that ramp, which is why it survived earlier validation; the cost is high-resolution R_meas (98.5 -> 101.9 shell-averaged). Removed dead code from add-then-remove churn - Prediction-time "still partiality" (unreachable: no setter), the phantom IndexingSettings::min_indexed_spot_fraction knob (getter, no setter - now the constant it always was), StillsPartialityRefine's caller-less Settings constructor and its reference to a long-gone env var, ProcessImage's unread bool return, an unused include, and a dead viewer overlay hook. Also - Viewer: the magnifier compared a QImage with itself, so its scene rect was set once ever and it could not pan into a larger dataset; the hover tail timer could fire after leaveEvent and resurrect the resolution readout outside the image. - update_version.sh regenerated the frontend lock file BEFORE bumping the version (every release shipped an off-by-one lock), and did git rm/git add on a path that has not existed since the client moved to src/client - with no set -e, both failed silently. - fpga/pcie_driver/postinstall.sh tested "[ ! occurrences > 0 ]", which is a redirect, not a test, so dkms add never ran. - Unit tests for the adaptive-threshold host functions, which had none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-27 09:07:00 +02:00
leonarski_fandClaude Opus 4.8	a8c1006c49	Choose min-pix-per-spot adaptively per image for serial-stills indexing ... For stills indexing the minimum-pixels-per-spot filter is now chosen per image instead of being fixed: the frame is indexed at min-pix 3/2/1 and the setting that maximises indexed-spot count weighted by indexed fraction (n_indexed^2 / n_total) is kept, then integrated once at that min-pix. The fraction factor keeps a smaller min-pix's extra spots only when the lattice actually explains them, so strong frames retain their real weak spots (extending resolution) while noise-flooded frames stay strict. The mode is selected by the presence of --min-pix-per-spot, now optional (SpotFindingSettings::min_pix_per_spot is std::optional<int64_t>): omit it for the adaptive per-image path, give a value to force a fixed min-pix. It applies only to the stills indexing path -- rotation indexing builds one global lattice and keeps a fixed min-pix, and the online receiver and the FPGA host path always carry a concrete value, so neither changes. IndexAndRefine::ProcessImage now returns whether the frame indexed, to drive the per-image selection. Exposed in the jfjoch_viewer spot-finding settings (adaptive-threshold and adaptive-min-pix checkboxes, each greying out the control it overrides); the broker uses neither. Validated on the full rotation regression battery (no regression) and the whole serial-stills target battery at full image count. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-26 18:31:35 +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	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