18 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	6e805f53c0	image_analysis: stop paying for work that is thrown away ... Three independent costs, each measured, none changing a result. Across the 37-crystal regression set the run time halves (median per crystal 2.0x, total 2.3x) and every crystal's merge statistics are unchanged. The image copy back from the device moved the whole preprocessed frame - 72 MB on a large detector, every frame, per worker - to serve a single host consumer that reads only the strong pixels, at most a few hundred kilobytes of it. Give the buffer a Gather() so that consumer asks for the values it actually wants (a host loop on the CPU, a small kernel on the GPU), and copy the frame back only when a CPU spot finder will genuinely read it. The copy the other way was worse: it came from an unregistered vector, so the driver staged it through its own pinned pool with a host-side memcpy on the calling thread, which does not overlap and collapses under concurrency - 11.6 GB/s at one worker, 1.6 GB/s at eight. That, not any hardware limit, is why throughput stopped improving past four to eight workers. Pinning the decompression buffer once per worker fixes it: on a 18 Mpx dataset the image loop goes from 13.6 to 7.9 ms per image at 32 workers, and 32 workers now beat 8 instead of losing to them. Ceres was computing seventeen partial derivatives where five are free. The per-image rotation refinement frees the beam and the orientation and holds distance, detector angles, rotation axis and cell constant, but the cost function declared all seven blocks, so every residual evaluated in Jet<17> arithmetic. A residual exposing only the two free blocks - the same arithmetic, the constants baked in - halves refinement, and it is exact rather than merely close: dual coordinates evolve independently, so the residuals and the free Jacobian columns are unchanged bit for bit. The merge sorted an index array with a comparator that dereferenced a 1.6 GB array of 72-byte records, i.e. a random walk over memory, single-threaded, twice per two-pass run. Sorting a packed key instead is 2.4x. French-Wilson allocated its integration scratch per reflection and ran serially; it now takes caller-owned scratch and runs over chunks, 4.2x. The correction surfaces re-tested every observation for usability and parity on each of ~22 passes and re-allocated their accumulators each time; bucket the indices once and hoist the buffers. Also convert std::round to std::rint where the rounded value only ever enters a squared residual. The tie rules differ - away from zero against to even - so this is safe exactly where a tie flips the sign but not the magnitude, and unsafe wherever the value becomes a Miller index; those sites keep std::round. Verified over all 2^32 float bit patterns: 8388608 exact ties exist, and the squared residual is bitwise equal for every one of them. Worth little on its own here, because the rounding that dominates is in candidate refinement, where the value is an index and the substitution is not available. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-01 21:35:28 +02:00
leonarski_fandClaude Opus 5	fb0272023e	scale_merge: apply outlier rejection to the anomalous split on the GPU path ... The GPU merge kernel rejects outliers on the device and keeps a per-full flag there, but only returned the per-group counts. The host array the CPU path fills stayed all zero, and the anomalous I(+)/I(-) accumulator is host-side and unconditional - so with --reject-outliers and a GPU present, the observations the merged IMEAN dropped were still averaged into I(+) and I(-). The same command on a CPU-only host excluded them: the exported anomalous differences depended on whether a GPU was there. R_meas was unaffected, having its own device-side path that reads the flags in place. MergeAccum now hands the per-full flags back so every host-side reduction sees the same rejections. The comment claiming reject_outliers was excluded from the GPU path was never true. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-31 14:53:17 +02:00
leonarski_fandClaude Opus 5	ffbf38d2ab	Rotation scaling: guard the per-frame scales whatever else is switched on ... The protection against a per-frame scale collapsing toward zero lived inside ComputeSmoothGWindow, so it only existed when smooth-G did: --smooth-g=0, a dataset whose oscillation width is unknown, and any caller that never sets a smoothing range - the viewer among them - merged with no guard at all. A collapsed G multiplies that frame's intensities by 1/G and its sigmas by the same factor, so nothing downstream can see it; the merge's n-sigma cut scales with the number that is wrong. Pull it out into ReplaceCollapsedScales, called unconditionally right after the partial scaling loop, and let the smooth-G window assume what it now guarantees instead of computing its own median and floor. The fulls guard built its median from every frame including those never fitted - those sit at the combine's corr = 1, so a run with many unfitted frames dragged the median toward 1 and the floor with it. It also reported the absolute amplification where the message says "below the run median". Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 17:51:44 +02:00
leonarski_fandClaude Opus 5	a95aca382c	Remove dead code left behind by recent changes ... None of this has a reader: - ScalingSettings::scaling_regularize and its setter/getter - ScaleOnTheFlyResult::succesful (never set) and ::time_s (set, never read), with the timing that only fed the latter - JFJochImage::last_fit_viewport_ (written twice, read nowhere) and the comment claiming the retry uses it - the retry keys off initial_fit_done_ - JFJochDiffractionImage::ice_ring_width_Q_recipA, and a QtConcurrent include in a file that uses none - an unused gemmi::Op accumulator in the spindle-angle helper - <random> in Merge.{h,cpp}, from before the half-set split became a hash - an orphaned comment describing the Ceres B-factor residual deleted in 014e43a4c, and two trailing comments that had collided on one line Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 11:29:42 +02:00
leonarski_fandClaude Opus 5	af97ad61e3	Rotation scaling: the search-only filters must not outlive their pass ... Two faults in the same block, both of which let a search pass corrupt the production merge that follows it. The device's corr was only copied back to the host for the diagnostic dump, but the |zeta| filter runs on the host and then uploaded the whole host array - so on a CUDA build it wrote the values ingested BEFORE scaling over the scaled and smoothed corr the device had just computed. With the rotation default --search-min-zeta 0.85 that means the space-group search was deciding the symmetry from an unscaled merge. Copy corr back first, and upload once after both filters instead. Zeroing corr also has no owner: it is how an observation leaves the merge, but the only thing that ever rewrites it is the scaling loop, which skips frames it cannot fit. A frame left with too few well-measured reflections therefore kept its dropped observations at zero for the rest of the object's life - and the final production merge re-uses the same object without re-ingesting. Snapshot corr before the filters and restore it at the start of the next pass, so each pass decides for itself and the final merge keeps everything, as documented. The frame rejection (--min-image-cc) is now applied on the host for both paths; its separate device path did nothing whenever the CPU combine was in use. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 11:12:13 +02:00
leonarski_fandClaude Opus 5	609650b061	Rotation merging: keep the systematic sigma floor when ISa is unmeasurable ... The cap that refuses to report an impossible ISa was zeroing the asymptotic b itself, and that same value is the floor passed to SigmaWithSystematicFloor - where zero means "no floor". So on the degenerate low-multiplicity fit the guard is written for, instead of capping merged I/sigma at 100 it removed the cap entirely. Report the asymptote as unmeasured, keep the fitted value for the floor. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 10:50:30 +02:00
leonarski_fandClaude Opus 5	6be94f2be0	Merging: do not subtract a negative intensity's Poisson term ... The expected-variance weights decompose an observation's sigma^2 into a background part and a Poisson signal part, then rebuild the signal part at the reflection's merged mean. The decomposition subtracted corr*I with I taken as-is, so a negative I ADDED to the background part: an observation at I = -1.5 with sigma^2 = 1 came out with a base variance of 2.7 rather than 1. That inflates the variance of precisely the down-fluctuated observations the correction exists for. Below about one photon they are then under-weighted and the merged mean is biased high - the same direction of error, in the same regime, that weighting by the observation's own sigma produces. Subtract max(0, I) instead: a negative intensity has no Poisson signal to remove. Both users of the decomposition are fixed - the stills merge, where expected-variance weighting is now the default, and the rotation combine it was mirrored from, which had it first. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-29 09:36:40 +02:00
leonarski_fandClaude Opus 5	f2b92e3f4d	rugnux: --search-min-zeta drops badly-measured observations from the symmetry search ... zeta is the sine of the angle between a reflection's rocking path and the spindle. Near 0 the reflection crosses the Ewald sphere almost tangentially, spends many frames in diffracting position and is measured worst. The de-novo space-group search asks how EQUAL an operator's paired intensities are, so its answer is dominated by whichever reflections are measured worst - and when the spindle lies in a lattice plane, an operator that permutes the two in-plane axes samples a different mixture of measurement qualities than one that only flips signs. That is not a fair comparison, and it can make a real symmetry operator look like a twin law. Measured on a thaumatin set mounted that way (its 4-fold is 88.9 deg from the spindle), the added operators' disagreement is 1.74x the parent's over pairs where both reflections have zeta < 0.85 and 1.003x - i.e. the symmetry is exact - over pairs where both are above it. The search consequently refuses the 422 promotion and merges the crystal in P222, while the same data forced to the right group give CC1/2 99.2% at multiplicity 10.7, matching XDS. With the option the de-novo pass ignores those observations (the final merge keeps everything - there completeness is the point): zeta cut observations ignored H ratio adopted 0 (off) - 1.47 P222 0.5 1620648 1.44 P222 0.7 3006013 1.34 P21212 0.85 4536724 promoted P4212 (correct point group) OFF BY DEFAULT, and it must stay off, because the same cut costs four other crystals their space group (P41212 -> P212121, I23 -> P2, I23 -> I222 twice): at 0.85 it discards 40-80% of all observations, which on a crystal whose geometry is not the problem simply starves the search. Two independent implementations - filtering the pairs that enter the statistic, and filtering the observations that enter the merge - trade exactly the same crystals, so this is a property of the cut and not of where it is applied. Verified bit-identical to the previous binary when off. The companion diagnostic is already there: the run now reports how close a symmetry axis lies to the spindle, which is the geometry that makes this option worth reaching for. Implementation note for anyone tempted by the cheaper route: excluding these observations from the ASU grouping alone does NOT work. The 3D combine selects partials on corr, not on their group, so their intensity still reaches the fulls and the merged intensities are unchanged - measured, the statistic did not move by 0.03 while 67% of observations were nominally excluded. Zeroing corr is what removes an observation from the combine, the merge and the error model alike. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-28 20:03:43 +02:00
leonarski_fandClaude Opus 5	4895dc1018	Rotation: let --min-image-cc drop frames that disagree with the merged reference ... The flag was accepted on rotation data and did nothing - it is read only by the stills merge (Merge.cpp), and the CLI warned about that rather than fixing it. Meanwhile RotationScaleMerge already COMPUTES a per-frame correlation against the merged reference and writes it to the per-image table; nothing acted on it. Wire the two together. A rejected frame has its partials' corr set to 0, which is how a frame already leaves the pipeline - every consumer requires corr > 0, so the combine, the merge and the error model all drop it together. The GPU path reuses the SmoothCorr kernel with a ratio of 0, so one implementation covers both. Off by default (0), and verified bit-identical to the previous binary when off. What it catches, on the two rotation datasets that have a population to catch: a two-lattice crystal - two lattices in two physical AREAS of the sample, so the sweep passes from one to the other and whole blocks of frames measure a different crystal from the one being merged (frames 500-700 index perfectly well at a per-frame CC of 0.22 against 0.47-0.56 either side, in 11 contiguous runs). R_meas 28.6 -> 24.6%, CC1/2 93.6 -> 95.1, high-shell CC 23.4 -> 38.3. a second dataset with 9.5% of frames below CC 0.30: R_meas 24.3 -> 23.4%, CC1/2 92.6 -> 93.4. The criterion is "this frame disagrees with the merged reference", NOT "this frame is off-crystal". It happens to catch both, because a frame that measures nothing and a frame that measures a DIFFERENT crystal fail the same test, and it does not need to know which. For the two-area case that is a workaround, not a treatment: it recovers one crystal by discarding the other, where processing the two as separate sweeps would keep both. The frame-block structure is clean enough that such a split could be detected automatically. WHY THERE IS NO DEFAULT. The per-frame CC is not comparable between datasets - it is as much a measure of data quality as of frame validity. Measured medians across the battery run from 0.30 to 0.81, so one absolute bound removes 13 frames from one dataset and 584 of 1800 from another: battery at --min-image-cc 30, 33 crystals: no point group changed (30/33), four crystals clearly better (one +5.4 CC1/2 points, the two-lattice case above, and ISa gains of 1.3-4.6 on three others) - and one healthy crystal lost a third of its frames and with them its high-resolution shell (CC1/2_hi 26.2 -> 2.0). This is the same trap as an absolute bound on any per-operator or per-frame agreement statistic, and the same one the per-frame scale guard avoids by measuring against the run's own median. A principled version would cut on the SHAPE of the per-frame CC distribution - a dataset with a bad subpopulation is bimodal, a uniformly weak one is not - rather than on an absolute value. Until that exists this stays opt-in, and the per-image CC it keys on is already in the _image.dat table for anyone choosing a value. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-28 11:45:49 +02:00
leonarski_fandClaude Opus 5	ec7a826136	Rotation scaling: guard the fulls refit against a collapsed per-frame scale too ... 704098712 guarded the per-frame scale on the partials, but it put the check inside ComputeSmoothGWindow - which only the partials path calls. Step 4 refits the scale from scratch on the COMBINED FULLS (Unity model, so corr is exactly 1/G), with no smoothing and no floor, and that refit was still free to collapse toward zero. It is the same failure and it is worse here, because there is no window average to dilute it: the collapsed frame's own fulls are multiplied directly. Measured on a dataset where the previous commit had already fixed the partials stage, the fulls refit put 1/G = 559x and 175x on two frames carrying 517 observations, and the merged CC1/2 read 26.2% where the intensities ENTERING that stage were fine - better, in fact, than the comparison run's in all ten resolution shells (R_meas 34.5% vs 39.5%, CC1/2 89.1% vs 83.0%). Reject a collapsed scale here as well, on the same measured criterion, and let those fulls merge unscaled - the state the combine left them in, and the same fallback the fit already uses for a frame with too few reflections. The check reads the host fulls after both the CPU loop and the GPU ScaleFulls, so one implementation covers both paths; the corrected corr is pushed back to the device exactly as the correction surfaces already do. THIS IS NOT A DETECTION-MODE PROBLEM. Over 8 configurations (both spot finders x 4 frame ranges) the separation is exact: every run with a collapsed scale had CC1/2 <= 58.5%, every run without had CC1/2 >= 74.1%, and nothing else predicted it. On one frame range it is the DEFAULT finder that collapses (CC1/2 58.5%) while the other is clean at 93.8%. The instability was never specific to the finder; it was latent in the scaling stage and either finder could trip it. Same 8 configurations, with this commit: finder A full 93.7 -> 93.7 (untouched) finder A -s 1 58.5 -> 91.3 (recovered) finder A -e 899 94.0 -> 94.0 (untouched) finder A -e 898 87.2 -> 87.2 (untouched) finder B full 26.2 -> 91.1 (recovered) finder B -s 1 93.8 -> 93.8 (untouched) finder B -e 899 8.1 -> 91.7 (recovered) finder B -e 898 74.1 -> 74.1 (untouched) Every collapse recovers; every healthy run is unchanged. The CC1/2 spread over the four frame ranges falls from 35.5 to 6.8 points for one finder and from 85.7 to 19.7 for the other - this dataset was not sampling a deep instability when its CC1/2 swung between 17 and 94 across frame ranges, it was sampling whether this bug happened to fire. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-27 23:08:50 +02:00
leonarski_fandClaude Opus 5	7040987125	Rotation scaling: do not trust a per-frame scale that has collapsed toward zero ... The per-frame scale enters every intensity as 1/G, and SolveScaleIRLS floors G at zero and nothing else. A frame whose fit is not determined by its data can return G ~ 0.002 against a run median of 0.865, and every observation it carries is then multiplied by ~500 - sigma by the identical factor, which is why no sigma-based outlier test can see it and why this looked for a long time like a partiality problem. (The 1/partiality path is in fact guarded: min_captured_fraction floors it at 0.7 by default on rotation.) The window smoothing that should have absorbed such a frame instead made it permanent. It averages log G over a window, so a scale collapsing toward zero does not merely corrupt its own frame - its logarithm drags the whole window down. Worse, where a run has a stretch of frames too sparse to fit at all, the only FITTED frames in a window can be the collapsed ones, and the geometric mean then averages the fault with itself. Measured on a multi-lattice dataset: frames 816 and 818 fitted G = 0.0023 and 0.0014 with every neighbour from 800 to 839 unfitted, so smoothing set G = 0.0018 across the whole neighbourhood - a 546x amplification. About 500 observations of 152000 (0.66%) then carried 99% of sum(I^2), and the merged CC1/2 read 17.2% where the same data with the classic finder read 93.7%. Treat a fitted scale far below the run's median as what it is - an undetermined scale, exactly like the too-few-reflections case the code already handles - rather than as a successful fit. Such frames no longer contribute to the smoothing mean, and a frame whose own scale is not credible takes the neighbourhood's, or the run's typical scale when the neighbourhood holds nothing credible either. The bound is a RATIO to the run's own median because the rotation per-frame G is not gauge-fixed: G and the group means have an exact global multiplicative degeneracy, and the fitted median drifts over 0.745-1.358 across the battery. An absolute floor would reject everything in a run that drifted low. MIN_CREDIBLE_SCALE_RATIO = 0.02 was chosen from measurement over 12 crystals in the default configuration, where the smallest legitimate min(G)/median(G) is 0.070; the failing case sat at 0.0017. It is 3.5x below anything real and 12x above the failure. Effect on the intensity tail of the failing case: max I 10224 -> 438, and the top 1000 observations' share of sum(I^2) 0.990 -> 0.421 (the classic-finder reference is 0.632, so the tail is now cleaner than the run this was compared against). Rotation battery, 33 crystals in the default configuration: ZERO crystals differ - no space group, CC1/2, high-shell CC or ISa change anywhere. The guard fires only on the pathology. It does NOT rescue that dataset: with the amplification gone its CC1/2 is 26.2% and R_meas 49.2% against the classic finder's 93.7% and 27.8%. Adaptive detection degrades those intensities for a second, independent reason that is still open. This commit removes a latent hazard for any run with a sparse stretch of frames; it is not the fix for that dataset. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-27 22:43:58 +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	c52886c8ff	Guard degenerate asymptotic-ISa fit on low-multiplicity data ... On very-low-multiplicity data (e.g. EP_cs_01-24, mult ~1.4) the merge has too few symmetry equivalents to measure the asymptotic I/sigma: both the (a, b) error-model fit and the per-group strong-reflection scatter collapse toward zero, so 1/error_model_b_asymptotic either explodes to an impossibly high ISa (tiny positive b) or is left as 0. Real macromolecular data does not exceed ISa ~50, so clamp the reported asymptote at a generous cap (ISa 100) and treat anything past it as unmeasured (result.isa undetermined) rather than emitting a spurious extreme. No-op for all well-measured data (b_asy well above the cap). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-21 23:02:40 +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