2 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	9f2696c1ac	Adaptive spot finding: the ring threshold replaces the floor, not the local test ... The self-calibrating finder was meant to replace the classic finder's FIXED PHOTON FLOOR with a per-resolution-ring threshold read off the image's own noise. As written it replaced the local-box SNR test as well, and that is the defect: a whole-ring threshold is an ABSOLUTE contour with no feedback from a pixel's own surroundings, so the area a spot puts above it grows as sigma^2*ln(peak/threshold) and never saturates. Measured on a strongly diffracting rotation set, the detected footprint grows by +8.05 pixels per e-fold of peak, so the brightest reflections came out as 100-500 pixel blobs and were then discarded for exceeding the size bound - every one of the ten strongest on an image. Intersecting with the local box gives -0.24 pixels per e-fold, the classic finder's own number to two decimals. WHY the local box is the right partner, rather than merely the incumbent: it is a prominence rule whose reference level is a 961-pixel mean. A spot inflates the box's own variance and the peak divides out of the acceptance test, so it cuts at a fixed FRACTION of the spot's own height. Referring that level to fewer pixels makes it inherit their shot noise - at FIXED footprint, estimating the level from 961 pixels, from 25, and from the single maximum gives centroid residuals of 0.524, 0.539 and 0.656 - so flat growth and a stable centroid turn out to be two ends of one dial. A contour on the bare maximum has the flattest growth of anything tried (+0.1) and merges worst. The two arms bind in different regimes, which is why intersecting beats choosing: on serial stills the ring threshold is 0.6x the classic floor, on this rotation sweep 2.3-6.0x. Stills are a strict no-op - 175 components against 175, identical per frame - so the +40% in stills indexing that the adaptive threshold was introduced for is untouched. What it buys, stated as one fact rather than two. Across five geometry pins spanning 1.1 mm it indexes the most frames of any arm tried, 0.831 against 0.803, and integrates 3.04 to 5.76% more observations - but those are the SAME number: regressing observation count on indexing rate over four arms leaves residuals of +/-0.7 percentage points against swings of -7 to +4.5%, so the extra observations ARE the extra indexed frames, not better data per frame. CC1/2, the only statistic here carrying per-observation quality, is +0.66 at one pin and -0.06 at the other: not harmed, not improved. <I/sigma>, ISa and R_meas cannot arbitrate on this data - across those pins each crosses zero as a monotone function of the pin. WHY an absolute contour indexes fewer frames, when its spot list is equal or better on every axis measured - recall, top-1000 recall, centroid, ice fraction, component count - is the interesting part, and it is not a detection effect at all: ITS OWN SIZE BOUND DELETES THE BRIGHTEST REFLECTIONS ON THE FRAME. A component is discarded because it grew past 200 px, and it grew past 200 px because it was bright, so the deletions are drawn from the head of the indexing budget rather than uniformly from it: they are 11x enriched in the top 250 of the thousand spots handed to the indexer, and the bound's own real deletions sit at MEDIAN RANK 12. Turning the bound off recovers 66% and 50% of the deficit at the two pins, against a bar registered at 33% before the run. Three of us dismissed this for most of a day on the grounds that the gates delete only ~4% of what is detected. That arithmetic was right and the denominator was wrong - a rate is not an impact when the thing being lost is selected for the property that makes it matter. Reworking the bound instead was measured and rejected: it recovers half the deficit, and it cannot be done without re-admitting what the bound is for - 68 components past 200 px, of which 8 are real and 60 are junk, where the intersect gets the 8 without the 60. The residual once the bound is off, +1.08%/+1.70%, is the contour itself. Component merging is ruled out separately: geometrically impossible here, 33.9 px minimum reflection separation against components spanning 10 px. So is a ranking effect - the intersect's lead runs +0.06% at --max-spots 250, +3.46% at 1000 and +14.26% at 2000, which is backwards for a selection artefact. Costs 0.48 ms per image in the finder, and 0.044 px of bright-spot centroid precision - measured convention-free, by fitting a line to a reflection's own centroid across five frames, after an XDS-referenced figure proved to be four fifths aperture convention. It also makes the compactness gate above it safe. On the absolute contour that gate is net damage, deleting 37 genuine reflections per ten frames; once the footprint stops growing nothing reaches its threshold at all. Also fixes a real but unexercised defect in PoissonThreshold, where the exact tail handed over to a normal approximation with a step. It changes nothing here: the clipped ring sigma is over-dispersed 1.2-4.9x against sqrt(mu) because it still contains diffraction, so the Gaussian arm wins every ring above mu=50 and none of the 522 thresholds move. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FBumeJVx4oeXxiBRpkrE5H	2026-08-28 15:30:39 +02:00
leonarski_f	538f3504d3	v1.0.0.rc-161 (#71) ... 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: significantly better quality of results, and faster.** A large rework of integration, scaling, merging, geometry refinement and space-group determination, together with measurements the program previously made no attempt at - the direct beam before indexing, the beam stop, the goniometer rotation scale, and the stretches of a sweep the crystal did not deliver. A rotation dataset typically gains observations at better <I/sigma> and R_meas, and every `mx` and `scale` run writes a `<prefix>_report.txt` results report modelled on XDS's `CORRECT.LP`. Many defaults moved with it: spot detection is self-calibrating, beam-stop detection and rotation geometry post-refinement are on, resolution limits default to as far as the detector reaches, and ice-ring handling engages only where the crystal is measured to have ice. * **jfjoch_viewer:** the beam-stop shadow, the detector calibration and the beam-centre measurement are reachable from "Analyze dataset"; the settings panel reports how the sample moved and how polarized the beam was; image rendering and interaction are faster. * **Performance:** bitshuffle+LZ4 images are decoded on the GPU rather than on the host, with the bitshuffle inverse fused into preprocessing so the decompressed frame is never held in device memory. * **Broker, writer, packaging and build:** image-slot lifetime and locking fixes, per-image datasets sized by the images actually written, the Debian/Ubuntu broker package renamed to `jfjoch`, and `image_analysis` compiling under MSVC again. **Breaking change to the rugnux command line:** * `--azint-only` and `--scale` are **removed**, replaced by `--mode azint` and `--mode scale`; the full pipeline is `--mode mx` and remains the default. A script passing the old flags now fails with the list of valid modes rather than silently running the wrong one. * `-t`/`--stride` is **refused on rotation data**: skipping frames cuts every reflection's rocking curve, so the combined fulls and their partiality would be measured over frames the sweep never recorded. Select a contiguous range with `-s`/`-e` instead. `--mode azint` and `--force-still` still take a stride. **Breaking changes to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.161, `frontend/src/client`) or read the affected fields as optional: * `image_scale_b` is removed from the `plot_type` enum, so a client requesting that plot now gets an error rather than a curve. * `azim_int_settings.high_q_recipA`, `spot_finding_settings.high_resolution_limit` and `spot_finding_settings.low_resolution_limit` are no longer `required`. All three mean "no limit at that end" when unset and are omitted from the response instead of carrying a placeholder value, which raises in a client generated from an rc.160-or-earlier spec. A value of 0 is still accepted and means the same thing. **Breaking changes to the stored formats** - a consumer reading these fields must treat them as optional: * The per-image image-scale B factor is no longer computed, so `/entry/MX/imageScaleBFactor` is absent from newly written HDF5 files and the corresponding key is absent from the CBOR DataMessage and END blocks. Files written by rc.160 and earlier still contain it and still open; nothing in the pipeline reads it any more. * `_reflns.jfjoch_diffrn_ISa` now carries the whole-range `1/sqrt(a*b)` that XDS's ISa denotes, and the error-model `a` and `b` are reported in XDS's convention; the strong-reflection asymptote moves to `_reflns.jfjoch_diffrn_ISa_asymptotic`. **A file written by an earlier version carries the asymptote under the plain `ISa` name.** Reviewed-on: #71 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-08-13 17:03:10 +02:00