201 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	b7a440bcbd	Docs: verified DOIs for Wilson (1949) and Whittaker; centre-of-symmetry references ... Both DOIs were resolved against doi.org/Crossref (title, volume and pages match), so the "DOI not verified" notes go. The analysis reference's References list gains Wilson / Howells-Phillips-Rogers and Baur & Kassner, whose methods 13.1 now describes (CLAUDE.md: a method described there is listed there as well as in ACKNOWLEDGEMENT.md). Every other DOI in ACKNOWLEDGEMENT.md, the CPU_DATA_ANALYSIS* pages, the RUGNUX* pages, README.md and the battery README resolves. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-05 16:34:59 +02:00
leonarski_fandClaude Opus 5.5	e2084895db	Docs: data-analysis reference brought up to the rc.174 behaviour ... Space group (13.1): every setting of a chosen rotation set is offered; screws are claimed at 8 nats, with how that bound was set; the P1 search merge is cut where a monotone fit of <I/sigma> drops under 1; the operator-homogeneity gate reads the R gap between a subgroup and the rest; a lattice-holohedral group is refused when merging under it narrows the L-test like a twin. Outliers (13.3): the rotation median is weighted at the expected intensity, and the band's systematic part is multiplicative, with its spread measured on the merge's own fulls. Indexing: a sparse lattice is integrated on every frame; pass 1's lattice is a hypothesis against a different re-index, and a pass sent back reuses pass 1's indexing. Image: the flipped axis sign must beat chance; the same-lattice beam-centre retry on an inconsistent merge. Integration: five correction surfaces, not four; the .hkl carries no amplitudes; the fulls' scale is smoothed differently from the partials'. Tutorial: the correction surfaces are cross-validated on the half-set correlation (as the reference says), not on an R_meas-like deviation. Overview: the footprint, the 5 A indexing hypothesis, the centre of symmetry, and the GPU pre-scan. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-05 16:34:31 +02:00
leonarski_fandClaude Opus 5.5	e7c4cb128c	Docs: results report - rejection counters, every CENTRE_STATISTICS key, build flags ... - OBSERVATIONS_REJECTED / _WILSON / _OVERLOAD: what each counts and how they relate (the overload count is not part of OBSERVATIONS_REJECTED). - CENTRE_STATISTICS_REFLECTIONS and the three per-statistic _F keys are named; NOT_APPLICABLE is stated as the code decides it (any of the three outside -0.3..1.3, or the control below 0.5). - BUILD_CXX_FLAGS no longer says that -march moves the results: the build turns floating-point contraction off and the indexer's reductions no longer depend on SIMD width, so CPU levels agree. The RUGNUX_GIT and BUILD_CXX_FLAGS keys were also listed twice in the header paragraph. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-05 16:32:36 +02:00
leonarski_fandClaude Opus 5.5	39abdb9f58	Docs: processing small-molecule data, and taking it into SHELXT / SHELXL ... Running Rugnux gains a "Small-molecule data" section: what the default run does about short axes, wide and split spots, sparse patterns, overloads and glide / centre-of-symmetry space groups, the two settings worth checking (polarization on a laboratory source, the resolution cut), and what the unmerged HKLF 4 file holds. Rugnux with other programs gains a worked SHELXT -> SHELXL route (instruction file built from the report keys, what SHELXL does with the unmerged file). The SHELXT/SHELXL commands were run on a battery set's output to check they work as written. The quick start's file list now includes <prefix>_detector.jpg, which every default rotation run writes. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-05 16:32:10 +02:00
leonarski_fandClaude Opus 5.5	d80579221b	Docs: Rigaku d*TREK SMV headers; SMV saturation is read where stated ... What Rugnux reads now describes the d*TREK vocabulary the SMV reader learned in this release (pixel size, image directions, 2theta arm, wavelength, encoded overflows), and no longer says that SMV never states a saturation value: CCD_IMAGE_SATURATION / SATURATED_VALUE are read where present. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-05 16:29:41 +02:00
leonarski_fandClaude Opus 5.5	db7cd6282e	Docs: repair sigma_rho / sigma_tau in the spot-footprint paragraph ... The backslash escapes \r and \t had been turned into a line break and a tab, which broke the LaTeX and split the paragraph. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-05 16:23:41 +02:00
leonarski_fandClaude Opus 5.5	09ba6d7225	CHANGELOG: rc.174 Rugnux entries most important first; SMV reader with the home-source battery sets ... Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-05 16:21:52 +02:00
leonarski_fandClaude Opus 5.5	ca8eff396a	CHANGELOG: rc.174 release notes ... Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-05 16:15:28 +02:00
leonarski_f	aa4455b18e	Merge branch 'rc174-all3' into rc174	2026-10-05 14:51:27 +02:00
leonarski_fandClaude Opus 5.5	9459444b6a	Viewer: link one libjpeg - drop Qt's JPEG and TIFF plugins ... With the static Qt of the Linux viewer, QJpegPlugin brings Qt's bundled libjpeg-turbo (3.1.4, JPEG_LIB_VERSION 80) next to ours from preview/ (3.2.0, ABI 62). Both export the same jpeg_* symbols and the linker silently kept Qt's, so WriteJPEGToMem - compiled against our headers - failed with "Wrong JPEG library version". In the viewer that aborted an in-process rugnux run at the end, where _detector.jpg is collected. The rc173 artifact shows it directly: jpeg_CreateCompress checks for 80 and the only libjpeg version string is 3.1.4. The viewer now excludes Qt::QJpegPlugin and the unused Qt::QTiffPlugin (which bound to whichever libtiff the link offered), and its clipboard copy and "Save image as JPEG" encode through WriteJPEGToMem instead of QImage::save. The Linux viewer CI job checks the binary holds no Qt JPEG/TIFF handler and exactly one libjpeg-turbo. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>	2026-10-05 12:47:55 +02:00
leonarski_fandClaude Opus 5.5	9d1650680e	Battery report: 8xtg's twin-immune zone is now read at the other twin laws' fraction ... Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-05 10:15:04 +02:00
leonarski_f	3167b4ce14	Merge branch 'battery-inhouse-model' into rc174-all3 ... # Conflicts: # docs/CHANGELOG.md	2026-10-05 10:14:54 +02:00
leonarski_f	0741b2b298	Merge branch 'dq-reg4' into rc174-all3 ... # Conflicts: # docs/CHANGELOG.md	2026-10-05 10:14:47 +02:00
leonarski_f	5575558c5f	Merge branch 'dq-reg3' into rc174-all3	2026-10-05 10:14:40 +02:00
leonarski_fandClaude Opus 5.5	f9ffc3d837	SearchSpaceGroup: ask a promotion's twin-immune zone on a twinned merge, read at the other twin laws' fraction ... 6iu9 (deposited P3_1, merohedrally twinned at 0.4 or more by its 321 law: H 0.097, CC 0.79) went from P3_1 to P3_121 when the penalised per-frame scale smoother (495f6a97b) landed; the ingest partiality fix alone (7d6c201e9) keeps P3_1. Bisected on the two binaries: smoother-only 6iu9 P3_121, partiality-only P3_1. The smoother only removed the luck: the P3_1 answer rested on the Lorentz-filtered arm's added-operator R contrast reading 0.71 against a bound of 0.72 (the all-observation arm already passed 32 at 0.82); better scaling moved it to 0.87, no gate refused, and the twin-immune zone - which reads -401 nats, acentric - is only consulted where a gate fired. A near-perfect twin passes every agreement gate by construction (H ratio 0.97 here); only the zone can refuse it. It was confined to refusals because a genuine trigonal crystal read -46 nats with no gate firing; on the battery 5uth (genuine P3_121, twinned by a 622 law, other-law CC 0.14) reads -206. The reason: the centric density was untwinned, but a twin by a law OTHER than the zone's operators reaches the zone as it reaches every reflection, so a genuine zone reads 0.81 at a = 0.2. The operators' own twin law cannot reach their zone, so only the centric side needs it. - TwinningAnalysis: the zone's centric density is the twinned one at a caller-given fraction (weighted sum of two chi^2_1, via exp(-y) I0(y)); the control's calibration expectation is taken at the same fraction (-KL(acentric || centric_a), -0.130 at a = 0 as before). At a = 0 nothing changes. - SearchSpaceGroup: twin_fraction_outside = the fraction implied by the strongest CC of a lattice rotation outside the group, relative to the group's own mean CC, through rho = 2a(1-a)/((1-a)^2+a^2); exported for the adopted group and used by Rugnux's TwinZoneVerdict and the zone report. - New Stage A test: a candidate that does not hold every lattice rotation, on a P1 merge whose <|L|> is in the partial-twin band [0.375, 0.44), is refused when the zone over one of its index-2 subgroups reads acentric by 20 nats (the TwinZoneVerdict bound), unless zones_ambiguous. The band's lower end is the L-test gate's: below it something else compresses the zones too (a pseudo-cubic small-molecule set, cuhf2, read its 422 zone at 0.64 beside a control at 0.58 and was turned to P222 without it). Zone evidence (calibrated, at the other-law fraction): 6iu9 32 -230 / -143 (refused, P3_1); 5uth +209 / +33 (P3_121 kept); 8xtg +324 / +65; 6vww P6 +20 / +8.5; 7k1l P6 +8 / +7.5. Battery (open+inhouse, targeted, against 20261004-2350 all2-full; only beyond-noise change listed): - 6iu9: fail -> pass, P3_121 -> P3_1, R_meas 17.4% -> 14.4%, ISa 4.6 -> 5.4, R-free 0.318 -> 0.327. - unchanged: 6iu5, 6iu6, 6iu8 (P3_1), 5uth, 5j23, insu_H_x06da_twin/notwin, 6vww, 7k1l, 8xte, 8xtg, 9i80, 4bwl, 2wnq, 8c3e, 2wnn, 2xfw, 5ebi, 6p8j, 6z9g, 6rlr, 6toc, 3mc4; 321/312 controls 5lzl, 6w4h, 9gqg, 6pxb, 9z72; all 14 small-molecule sets (cuhf2 checked again after the band). - private subset (8 sets): no change beyond noise. Tests: [twinning] (new: zones read at the other twin laws' fraction), SearchSpaceGroup*. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-05 10:13:50 +02:00
leonarski_fandClaude Opus 5.5	636c6a3067	SearchSpaceGroup: operator-homogeneity gate reads the R gap between a subgroup and the rest ... The gate that refuses a point group whose own operators "disagree among themselves" read worst-agreeing over best-agreeing operator R. That divides by an extreme order statistic - the pole the contrast gate was introduced to remove - so a genuine group whose operators merely spread in a continuum is refused as soon as one operator happens to agree unusually well. That is what refused 432 on a private cubic F432 crystal after the overload drop (37a8c8e24; bisected: that commit alone gives F23, b126b9fc1 does not change the search). The crystal's intensity-weighted R is dominated by a few dozen strong low-order reflections. Dropping the overloaded ones (whose flank-extrapolated values disagreed ~2x with their mates) raised every operator CC and made the cleanest 432 operator cleaner still, while anisotropic systematic error keeps the genuine 23 operators spread ~2x among themselves: worst-over-best went 2.68 -> 4.0 against the 3.2 bound. H ratio (1.25) and contrast (0.78) passed throughout. A mixture of real and false operators is specific: the real ones form a subgroup (the true group's intersection with the candidate) and everything outside it is false. The statistic is now the largest factor by which every operator outside some subgroup reads worse than every operator inside it - a gap, found by walking the operators sorted by R and reading each prefix that closes into a group. It is never above worst-over-best, so nothing admitted before can be refused; the bound stays 3.2. Read off the operator tables of the all2 full battery and run 3: genuine adopted groups reach at most 2.5 (the cubic crystal 1.8-2.0), the 5ebi 622 mixture reads 3.6 (was 6.0), 9hnc's false 422 3.4, and 2wnn's false 222 3.8 (unchanged, still refused by this gate). Targeted runs vs all2-full (f64f76): the private cubic set F23 -> F432 (pass); every other set identical to the last digit - five other private sets; open 5epe 8sqt 3inp 9fhc 6oel 7orr 8tyy 3ky7 6h5t 6moj 2wnn 5ebi 9hnc; lyso_x06da_ref, lyso_x06da_5keV, myob_x06da_split; all small-molecule sets (citric R1 .0374, aspirin .0363/.0358, hepes .0310, yag .1021, kdp, lcystine, cytidine, dnba, lalanine, metformin, nidppe, cuhf2); and the high-spread trigonal/ tetragonal/hexagonal panel (insu_H twin/notwin, insu_I weak/low_isa, 6v2r, 8xtg, 5j23, 6iu6, 6iu8, 3mc4, 6vww, 7k1l, 9i80, 6pxb, 9hs7). SearchSpaceGroup* and [SearchSpaceGroup] test cases pass. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-05 09:29:18 +02:00
leonarski_fandClaude Opus 5.5	a628f06868	Space-group search: an ask that promotes over a twin-gate refusal is decided by the twin-immune zone ... Open set 5ebi (deposited P2_1, a = c and beta = 120: a monoclinic crystal on a hexagonal metric, pseudo-merohedrally twinned, <|L|> 0.433) regressed from P2_1 to C222_1 with dq-sm2-rest baf2017c9. Of that commit's two changes it is the sub-lattice ask's R-contrast operator test, not the hot-patch mask: 5ebi is a CCD (.img) sweep, so HotPixelFinder never runs on it. Without the R contrast every metric two-fold that passes min_operator_cc was kept, LePage closed them into the whole hexagonal metric and no sub-lattice ask was made. With it the false hexagonal two-folds drop out, the two in-plane two-folds of the C-centred orthohexagonal cell survive (CC 0.97, R 0.061 against 0.045 for the genuine screw: contrast 0.96), and the ask on that sub-lattice adopted C222_1. The main search had refused 622 on the added-operator R (contrast 0.70 against 0.72), but the ask's own search cannot see that: the gates there are relative and the twin law passes them on its own. Stage A's L-test-under-merge gate does not reach it either - C222_1 is not holohedral on a hexagonal metric - and read per operator it does not separate it: merging under the in-plane two-fold moves <|L|> only 0.425 -> 0.418 (14% of the gap to 0.375). Fix: where a twin gate of the search in hand refused a higher group, an ask that would promote re-opens what that gate answered, so it is arbitrated as every other promotion over a refusal is - by TwinZoneVerdict on the operators it adds over the group in hand (that group carried into the ask's setting). Acentric with margin and the group in hand stands. 5ebi: zone 222 over 2, n 1865, calibrated -23.9 nats -> twin law, P 1 21 1 kept. cuhf2 (the case baf2017c9 fixed) has no twin-gate refusal in hand, so its zone is not read and P422 stands. Targeted battery vs the rc174-all2 full run (20261004-2350_f64f76_all2-full), same base: reg4-v1 (32 sets: 5ebi, cuhf2, sub-lattice sets 6iu6 6iu8 6iu9 6z8o 8t7r 9ea5, twinned/pseudo- merohedral 9hnc 3meb 2wnn 2xfw 2wnz 4bwl 2wnq insu_H_x06da_twin, controls lyso_x06da_ref thau_x10sa_0p1deg 5reo, all 14 small-molecule sets): only 5ebi changes - C2221 -> P1211 (pass), ISa 10.9 -> 14.8, R_meas 12.3% -> 10.2%, R_free (deposited model) 0.571 -> 0.537, cell dev 40% -> 0.05%. Every other set identical in space group, ISa, R_meas, R_free, d_min and SHELXL R1. reg4-v1b (the 12 other open/in-house sets whose run adopts a metric or sub-lattice ask): identical. Private arm (the 7 sets whose mask changed with baf2017c9 and the 4 that take an ask): identical. Still failing as before: 4bwl, 2wnq (near-perfect twins, C222_1 via the metric ask with no refusal in hand), 6iu9, 9hnc, kdp. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-05 09:06:16 +02:00
leonarski_fandClaude Opus 5.5	7eb8e93a0a	Rugnux --model: report the anomalous map's mean height at the model's anomalous scatterers ... ANOMALOUS_SCATTERER_MEAN_SIGMA= is the anomalous difference map, read at every model atom from phosphorus up (S of Met/Cys, metals, Cl, I) with the same cubic interpolation as ANOMALOUS_SITE_*, averaged in map sigma; ANOMALOUS_SCATTERERS= is their count. One number for the anomalous signal of a merge that does not depend on which ten atoms come out on top - what the battery tracks for the long-wavelength standard-protein sets. A new key only: no report version bump. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-05 07:56:32 +02:00
leonarski_fandClaude Opus 5.5	f64f764d40	Merge branch 'dq-kdp-int' into rc174-all2 ... Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 23:49:16 +02:00
leonarski_fandClaude Opus 5.5	0e35cad1e2	Docs: split reflections in the measured footprint ... Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 23:32:29 +02:00
leonarski_f	9223c27c1b	Merge branch 'dq-sym-glide' into rc174-all2 ... Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB # Conflicts: # docs/CHANGELOG.md	2026-10-04 23:29:11 +02:00
leonarski_fandClaude Opus 5.5	98f678ae89	Merge branch 'dq-sm2-rest' into rc174-all2 ... Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 23:29:07 +02:00
leonarski_fandClaude Opus 5.5	01c7d4636b	Merge branch 'dq-sm2-int' into rc174-all2 ... Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 23:29:07 +02:00
leonarski_fandClaude Opus 5.5	60b7fb86fa	SearchSpaceGroup: glide groups without a centre of symmetry; the centre decided by absences, a default, or the intensity distribution ... Non-Sohncke candidates were enumerated only when their PROPER rotations equalled the measured point group's, which only centrosymmetric groups satisfy. Groups without a centre (Pc, Pna2_1, I-42d, I4_1md, Fdd2, P-42_1c, I-43d) were never candidates: where a centrosymmetric group shares their absences rugnux wrote it silently (Pc -> P2/c), and where none does the dead glide zone was dropped and a Sohncke subgroup written (KDP-type I-42d data -> I4_122). - Enumerate non-Sohncke groups by Laue class. The Sohncke-signature dedup, CellHostsRotations and the glide-evidence bar are unchanged. Groups with identical absences in the same Laue class are scored once and carried as `same_absences`; a selected candidate brings them into `alternatives`. - Convention for which twin is written: the centrosymmetric one where it exists (missed centres are the common error, Baur & Kassner 1992), otherwise the lowest-numbered (I4_1md over I-42d). - The centrosymmetric default gives way only when, on the general reflections of the Laue class of the final merge, <|L|>, <|E^2-1|> and N(0.1), each calibrated against acentric/centric intensities simulated with the reflections' own sigmas (fixed-seed mt19937_64, own deviate transforms), read acentric (L f <= 0.3, others <= 0.5), every f lies in [-0.3, 1.3], the always-centric control reads centric (f >= 0.5), and the lattice excludes twinning (gemmi Le Page metric admits no rotation beyond the Laue class, no TWIN_DOMAIN leftover lattice). Then the group is switched and re-merged. - Report: SPACE_GROUP_CENTRE (IMPLIED_BY_ABSENCES / ABSENT_BY_ABSENCES / NOT_DETERMINED / ABSENT_BY_STATISTICS), CENTRE_TWINNING_EXCLUDED, CENTRE_STATISTICS_* on every searched run, and prose for the absence-equivalent alternatives. Battery (targeted): all 14 small-molecule sets vs 58a4bf (smt-all, kdp-all): every group unchanged except kdp_x10sa_20keV I 41 2 2 -> I 41 m d with I -4 2 d as the alternative; dnba stays C 1 2/c 1, now NOT_DETERMINED with C 1 c 1 listed (statistics read centric, f 0.96-1.24). The P2_1/c, Pbca and Ia-3d sets read IMPLIED_BY_ABSENCES with no alternative. Protein panel (19 sets, twinned panel + controls, run glide-prot): every space group equals the rc174-all base (3r6o re-run with the base binary: I 41 2 2 both); no SPACE_GROUP_CENTRE on any. Twinned proteins read the centre statistics NOT_APPLICABLE (L f -0.3 to -1.7) or ACENTRIC. Private subset (8 sets): 8/8 groups unchanged vs 58a4bf. The glide-zone evidence scan over battery 3 (every non-Sohncke group of each run's Laue class, centrosymmetric or not) peaks at 0.69 nats/reflection on proteins against the 2.0 bar. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 23:18:02 +02:00
leonarski_fandClaude Opus 5.5	b126b9fc15	Rotation merge: scale from the fulls alone only where that leaves an error model ... The per-frame scale was fitted on the partials from 50 rocking events per frame and taken from the fulls alone below. The counts of small-molecule sweeps (3-43) and proteins (5-900) overlap, and a weak protein at 36 events per frame scaled from its fulls had no resolved error model at all (ISa undetermined, d_min 5.10 A) where its partials gave ISa 32 and 4.88 A. The first merge of a pass that is not a space-group search is now made both ways, and the count stands as the prior unless its merge has no resolved error model while the other merge has one. Search merges (P1 / subgroups) take the prior. The two ISa values are deliberately not compared beyond that. Tried as the arbiter, "higher ISa wins" (and weighted R_meas as fallback) agreed with the external yardsticks on 10 of 11 crystals but chose the partials on a 6-events-per-frame small-molecule sweep: ISa 10.5 vs 8.7, weighted R_meas 0.102 vs 0.115, SHELXL R1 0.105 vs 0.062 - the partiality error the partial scale absorbs is shared by symmetry mates at the same rocking geometry, so their agreement cannot see it. Statistics of the difference between the two arms' frame scales did not separate that sweep from the proteins that want the partials either. Effect: only crystals whose prior arm fails change; every small-molecule set and every protein control keeps its arm. Private weak protein: ISa undetermined -> 32.3, d_min 5.10 -> 4.88 A, weighted R_meas .343 -> .337. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 21:03:02 +02:00
leonarski_fandClaude Opus 5.5	37a8c8e24e	Rotation merge: drop rocking events with an overloaded pixel; capture uncertainty in the merge variance ... A saturated pixel in a spot means the brightest part of the reflection was not measured. The integration used to drop the peak frame's partial (its peak pixel is unreadable) and keep the flanks, so the combine extrapolated the event from its tails by the partiality model: on a strongly diffracting small-molecule crystal the strongest low-order reflections read 2-3x low and were the largest SHELXL misfits. XDS drops such a reflection (OVERLOAD); so does rugnux now. - Integration (CPU + GPU engines): a reflection is `overloaded` when a signal-disk pixel is saturated, or unreadable on this frame but not in the run's pixel mask - EIGER/PILATUS write their error value for a pixel they could not count, which the preprocessor turns into a masked pixel like a gap's. The engines now receive the PixelMask to tell the two apart (an earlier attempt that re-classified the marker as saturation in the preprocessor broke a dataset whose gaps are not in the file's mask). An overloaded reflection is kept with its box sum, unfitted, only so its event can be recognised. - Rotation combine (CPU + GPU): an event with any overloaded partial is dropped whole; counted in the log and the report (OBSERVATIONS_REJECTED_OVERLOAD=). The unmerged MTZ export drops it too. - Everything else that reads reflections leaves an overloaded one out: AcceptReflection (stills merge, per-image scaling), the post-refinement gather, the axial-row sums. - Capture uncertainty: the merge rebuilds each full's variance at the reflection's mean (counting_variance / ModelSigma) and dropped the capture term the combine had put into sigma, so a full extrapolated from part of its rocking curve merged at the weight of a whole one. Fulls now carry it (Obs::capture) and the rebuilt variance adds (capture * <I>)^2, host and device. SHELXL R1 on rugnux's own integration (harness), median fix -> this: citric acid .0648 -> .0420 (XDS .051; 221 events dropped, EXTI 1.02 -> 0.29), HEPES .0396 -> .0381 (184), aspirin 20 keV .0387 -> .0385 (6), aspirin 25 keV .0376 -> .0375 (5); metformin/nidppe/dnba/lalanine/cytidine no overloads, unchanged. YAG .116 -> .128 (87 dropped; its scale loop does not settle either way). Proteins and private subset: see the branch report. Tests: BraggIntegrationEngineCPU_SaturatedPeakIsFlaggedNotDropped (new), BraggIntegrationEngineGPU_MatchesCPU (overloaded flag compared), AcceptReflection_ResolutionLimits, [write_reflections], [large]. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 21:01:40 +02:00
leonarski_fandClaude Opus 5.5	c3be6c6bcb	Docs: persistent hot-pixel patches are masked as well ... Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 20:42:26 +02:00
leonarski_fandClaude Opus 5.5	70fe5d2af2	Docs: the footprint stencil reaches 4 sigma ... Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 20:32:03 +02:00
leonarski_fandClaude Opus 5.5	1903b8688d	Battery: L-alanine is scored against its 100 K ambient-pressure structure ... The open-arm L-alanine set's COD reference (2104782) is a 0.2 GPa room-temperature diamond-anvil-cell structure (372 reflections, 43% complete), not the ambient one the docs called it. The set's own cell (5.787 5.940 12.263) is the 100 K ambient form, so the reference is now COD 2311261 (100 K, 5.791 5.944 12.269; Parsons, Flack & Wagner, Acta Cryst. B69 (2013) 249-259). SHELXL's refined R1 does not depend on the starting model (0.0546 vs 0.0524), but the fixed-model R1(F) the battery reports goes from 0.168 to 0.087, so that number now measures the data rather than the pressure difference; cell_dev_pct likewise compares against the right cell. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 17:03:05 +02:00
leonarski_f	4c7d8a0385	Merge branch 'dq-sym-screw' into rc174-all ... # Conflicts: # docs/CHANGELOG.md	2026-10-04 15:58:43 +02:00
leonarski_f	0c5ac8c8e5	Merge branch 'dq-sm-scale' into rc174-all	2026-10-04 15:58:36 +02:00
leonarski_fandClaude Opus 5.5	ac179e549e	Rotation scaling: reconcile with the ingest partiality fix; no flux on the fulls-only path ... Merged dq-sm-absorb, whose ingest fix (corr_ingested carries the recomputed partiality, not the predictor's) repairs the same defect as this branch's unit partial scale on the path without partial scaling. The two did not double-apply - the unit scale rebuilt corr from scratch - but they differ by the incident flux, and measured head to head the flux costs the sparse sweeps: SHELXL R1 on four in-house organic sweeps 0.0459/0.0396/0.0709/0.0413 with it, 0.0421/0.0393/ 0.0697/0.0405 without; on five open small-molecule sets equal or better without (0.0707 -> 0.0660 on one). Only the cubic absorbing sweep prefers it (0.119 vs 0.139): there the background really does fall with the absorbed beam. So the unit partial scale and its device kernel are removed and the ingest fix stands alone; the flux meter's smoothing, which only mattered on that path, is reverted, so the partial-scaling path sees the flux exactly as before. The penalised per-frame scale of the fulls stays. Also restores two characters of CPU_DATA_ANALYSIS_INTEGRATION.md that the previous commit's rewrite had turned from a stray carriage return into a line break. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 15:43:15 +02:00
leonarski_fandClaude Opus 5.5	4979f8aa68	French-Wilson: anisotropic Wilson prior from the fitted anisotropy tensor ... The French-Wilson prior of each reflection is now epsilon * K_shell * a(h), with a(h) = exp(-1/2 s^T B s) from the deviatoric tensor AnalyzeAnisotropy already fits (the form it is fitted in) and K_shell = sum(I/eps) / sum(a), so a shell's priors still average to its measured mean. The amplitudes are made isotropically at the merge as before and made again once the tensor exists (full pipeline and --mode scale). Only F/SIGF and F(+)/F(-) change; IMEAN/I(+)/I(-) are bit-identical. Applied whenever a tensor was fitted, with no detection gate: a near-isotropic tensor gives a(h) ~ 1 and the isotropic prior back, and the prior wants the best estimate of <I> along h whatever its cause. Follows ctruncate's anisotropic prior (Ballard & Stein, CCP4); credit in ACKNOWLEDGEMENT.md, CPU_DATA_ANALYSIS.md and at the algorithm. --model scaling (ModelScaling.cpp) was checked: k_overall + symmetry-constrained anisotropic B + flat bulk solvent fitted on the working set, against the same FW F written to the MTZ - as REFMAC/phenix.refine do. No change needed. Evidence (REFMAC 10-cycle restrained refinement of the deposited model, R-free on the depositor's free reflections shared by both data sets; base = rc174 processing, same IMEAN): set base new d set base new d 9rcs 0.3475 0.3494 +0.0019 8qq7 0.4452 0.4503 +0.0051 9yzk 0.3192 0.3171 -0.0021 9hs7 0.2898 0.2465 -0.0433 6yqf 0.4642 0.4543 -0.0099 5nw5 0.3256 0.3206 -0.0050 7n2s 0.3126 0.2998 -0.0128 6z8o 0.2927 0.2892 -0.0035 6qaj 0.3390 0.3038 -0.0352 6moj 0.2756 0.2651 -0.0105 6r72 0.3826 0.3797 -0.0029 7qij 0.3239 0.3140 -0.0099 anisotropic sets: median -0.0075, mean -0.0107, 10/12 better isotropic controls: 5reo -0.0014, 7kcn +0.0003, 6fid +0.0002, 11if 0.0000 rugnux's own --model R-free moves the same way (median about -0.019; 5nw5 +0.006), R_model shell-scaled too; dep_cc_delta unchanged (intensity based). The adoption rule (median gain >= 0.005 on the anisotropic sets, no control worse than +0.002) is met. The two sets that lose are the one with a FLAT resolution signature (8qq7) and 9rcs, where the exp form drives the dead direction's prior to ~0 beyond 3.7 A. For scale: ctruncate's own anisotropic prior on the same merges moved the same REFMAC R-free by a median of only -0.0008 (9hs7 +0.026). Inhouse lyso_x06da_ref, thau_x10sa_0p1deg: every battery metric unchanged. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 14:24:14 +02:00
leonarski_fandClaude Opus 5.5	495f6a97b3	Rotation scaling: penalised per-frame scale of the fulls; fulls-only partials get flux and partiality ... Three defects in the per-frame scaling of sparse (small-molecule, weak) rotation sweeps: 1. The fulls' per-frame scale pooled sparse frames by their RAW full count, but in a high-symmetry group with many systematic absences most usable counts stayed under the minimum, so most frames were never fitted and kept corr = 1 beside pinned, fitted frames (two gauges in one reference). The release step then read the gauge offset (a constant 134x on a cubic Ia-3d small-molecule sweep) as signal and gave each frame exp(kept_f * 4.9) - the e^-5 errors on a quarter of the frames, R1 0.62. A fixed box window also cannot follow a 100x absorption ramp over a few degrees, and frames under the credible floor, exempt from the window, ran away to 1e-7. Now each round fits every frame on its own fulls (no pooling, no minimum), and the scale is a penalised second-difference smoother of log G (Whittaker/Eilers), each frame at the information of its fit, lambda by cross-validation over blocks one rocking curve wide (interleaved single frames leak through shared rocking curves and chose to follow every frame). After convergence the existing ShrinkToRestrained hands back the per-frame deviation its neighbour shares. Pooling and the box window are gone from the fulls loop; the partials loop is unchanged. 2. With partial scaling off (< 50 rocking events per frame) the partials kept the integration-time corr: no incident-flux correction and not the partiality of the ingest-smoothed geometry, because only the partial scaling loop rewrote corr. They now get corr = prescaling_corr / partiality at G = 1 (host, and a device kernel). 3. The flux meter (per-frame mean background) jumped 30x between neighbouring frames of a sparse sweep - on a few reflections it measures which reflections the frame holds. It is read through the same smoother at the precision of each frame's mean. SHELXL R1(>4sig) against the published structures, rc174-cand -> this, on the in-house small-molecule sweeps: cubic Ia-3d 0.615 -> 0.119 (XDS 0.088); four organic sweeps (monoclinic / orthorhombic) 0.0515 -> 0.0459, 0.0451 -> 0.0396, 0.0747 -> 0.0709, 0.0452 -> 0.0413; ISa up to 11.6 -> 31. Raw flux instead of smoothed costs 0.002-0.003 R1 on the first two. A weak, decaying protein sweep on the fulls-only path: ISa 6.7 -> 27.1. CPU and GPU paths agree. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 14:18:08 +02:00
leonarski_fandClaude Opus 5.5	20d5146544	Docs: changelog and decisions page for the two screw-axis changes ... Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 13:25:17 +02:00
leonarski_fandClaude Opus 5.5	fc4bbab8e2	v1.0.0-rc.174 ... Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 12:03:29 +02:00
leonarski_f	e72236b08d	Merge branch 'battery-drop-7udi' into rc174-cand	2026-10-04 11:26:58 +02:00
leonarski_fandClaude Opus 5.5	9c0a8c740c	Battery: drop 7UDI from the open arm ... Its deposited sweep lacks 40 deg (frames 561-720 are not in the archive; the depositors processed it as two sweeps), so it tests gap handling rather than processing. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 11:09:25 +02:00
leonarski_fandClaude Opus 5.5	f0349949d6	Battery: ten open-arm sets from under-represented facilities and beamlines ... SRS Daresbury PX10.1 (6RYM), EMBL Hamburg DORIS X13 (7BGU), NSLS X29A and X25 (8V4J, 8V2T), ESRF ID14-2 (5JK4), Australian Synchrotron MX2 (6CS9), CLSI 08B1-1 (7UDI), SSRF BL17UM (9LXL), MAX IV BioMAX (9S02), ALBA XALOC (6GVK) - marCCD, ADSC (Quantum 4/210r/315), PILATUS and EIGER2 files. Each read and processed with the current rugnux; 7BGU (C2 imposed on a P1 lattice) and 7UDI (P41 under-called to P2) disagree with the deposition. Multi-sweep archives pinned to one sweep. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 09:57:45 +02:00
leonarski_f	86ca86f1d1	Merge branch 'hkl-unmerged-fulls' into overnight-cint	2026-10-04 03:41:26 +02:00
leonarski_fandClaude Opus 5.5	a6378800b8	Footprint integration: GPU/CPU parity sections, docs, changelog ... BraggIntegrationEngineGPU_MatchesCPU gains three footprint sections (spaced, crowded under overlap exclude, with the radial background correction): both engines classify the summation ellipse, the grown ring and the footprint Gaussian alike. Integration chapter and changelog describe the measured footprint. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 02:42:09 +02:00
leonarski_fandClaude Opus 5.5	9874db5d7f	rugnux: .hkl holds the unmerged scaled fulls on rotation data ... The SHELX HKLF 4 file now has one record per full reflection - its partials summed, the per-frame scale and every correction applied, sigma(I) as the merge weighted it - at the index it was measured at, not averaged with its equivalents: the chemical crystallographer's convention, so SHELXL computes Rint and Rsigma itself. Outliers the merge rejected and fulls beyond its resolution cut are left out; no batch column (it would select a BASF scale in SHELXL). The engine hands the fulls back only for a merge that may be written (RotationScaleMerge::SetExportScaledFulls), so the search merges, the pre-pass and the P1 cross-check carry no copy; the fulls follow the same relabelling as the merged reflections (merge_to_written). Stills keep the merged file. --mode scale writes the unmerged form too. Validation: p.mtz md5 unchanged on myob/cytc/thau (GPU). SHELXL on the same runs, merged-old vs unmerged-new (COD models, harness /data/tmp/sm_shared): aspirin 20 keV Rint 0 -> 0.071, Rsigma 0.036 -> 0.043, R1 0.0964 -> 0.0969, wR2 0.312 -> 0.310, GooF 1.53 -> 1.47; HEPES 20 keV Rint 0 -> 0.163, Rsigma 0.057 -> 0.068, R1 0.0903 -> 0.0897, wR2 0.318 -> 0.263, GooF 1.57 -> 1.10; the "input data appear to be merged" warning is gone. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 01:16:50 +02:00
leonarski_fandClaude Opus 5.5	2c97e654ed	Battery: add two L-cystine sweeps (in-house arm); say which open sets are pink beam ... lcystine_x10sa_20keV and lcystine_x10sa_25keV are scored against the literature structure only (hexagonal L-cystine, P 61 2 2, COD 5000005, Oughton & Harrison 1959): XDS indexes under 10% of the spots of either sweep, with the cell supplied and with the spot range cut to 150 frames, so there is no CORRECT.LP to take a reference from. On the current build the 25 keV sweep passes (P 61 2 2, cell within 0.5%) and the 20 keV sweep finds no lattice. EXTERNAL_TEST_DATA.md: none of the open-arm datasets is pink beam; every PDB record is single-wavelength (9Q41 used a multilayer monochromator). The pink-beam sets are the in-house ones. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>	2026-10-02 16:27:52 +02:00
leonarski_fandClaude Opus 5.5	f06780bd91	Battery: record each set's wavelength; add the rc173 battery report to docs ... Every open and in-house manifest row now carries `wavelength` (A), taken from WAVELENGTH in rugnux's own p_report.txt of the latest run of that set (the full rc173 run 20260929-2003 plus the two 10-02 runs for the sets added since). Descriptive only; the scorer ignores it. docs/BATTERY_REPORT.md is report.md of the full rc173 open + in-house run (210 sets), verbatim, to be polished. The private arm runs separately and has its own report, so nothing from it appears here. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>	2026-10-02 16:06:13 +02:00
leonarski_fandClaude Opus 5.5	dcc710a226	Battery: eight more home-source sets (open arm), five small molecules (in-house arm) ... Open arm, all IRRMC, single Cu K-alpha sweeps on Rigaku Saturn CCDs read through the d*TREK SMV path: 3mc4 (H 3), 3meb (P 1 21 1, Saturn 944, overflow ratio 32), 3p85 (P 63 2 2), 3r6o (I 41), 5uth (P 31 2 1), 5vml (P 42 21 2), 6cee and 6v2r (P 21 21 21 / P 41 21 2, Saturn A200, unbinned 2048x2048, 0.1 mm pixels). Detector 2theta spans -10 to +10 deg. Run 20261002-1326_84228b_home-source-12: all pass except 3r6o, called I 4 2 2 against the deposited I 41 with twinning suspected (<|L|> 0.32). Two further candidates (3r6h, 3sgw) were dropped: what the repository lists as one dataset is two sweeps under one file template, split by a phi change, which the reader refuses. In-house arm: aspirin (20 and 25 keV), anhydrous citric acid, HEPES and YAG, measured at X10SA. The reference is XDS's CORRECT.LP (refs --write) with the space group taken from the literature as ref_override, because XDS reports only Sohncke groups; each override cites its COD entry and paper. Run 20261002-1354_84228b_small-molecules-inhouse: four pass, including HEPES as P b c a where XDS has P 21 21 21; YAG is called I 41 3 2 against I a -3 d (both programs merge it poorly, rugnux CC1/2 0.40, XDS ISa 3.2). EXTERNAL_TEST_DATA.md gains the eight depositions (DOIs checked on DataCite) and updated counts; the battery README lists the small-molecule standards and has the current count of symlinked open-arm directories (42). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>	2026-10-02 13:57:30 +02:00
leonarski_fandClaude Opus 5.5	ac7c6af5a8	Read Rigaku d*TREK SMV images; add two home-source sets to the open battery ... The SMV reader only knew the ADSC vocabulary, so a Rigaku Saturn frame was recognised as SMV and then refused for want of PIXEL_SIZE. A header naming DETECTOR_NAMES is now read as d*TREK: - pixel size and the point of normal incidence from <det>SPATIAL_DISTORTION_INFO; - image directions from <det>DETECTOR_VECTORS combined by <det>SPATIAL_DISTORTION_VECTORS, matched to a DetectorOrientation (a Saturn 944+ image is mirrored and turned a quarter, so the hand is preserved); - distance and the detector circles (2theta etc.) from <det>GONIO_*, composed into PONI angles; spindle from ROTATION_VECTOR, angles from ROTATION; - wavelength from SCAN_WAVELENGTH, or the second number of SOURCE_WAVELENGTH (the first is a count - the old NumAny fallback would have read 1.0 A); - pixels above 32767 decoded as (v - 32768) * RAXIS_COMPRESSION_RATIO. dxtbx's FormatSMVRigakuSaturnNoTS, which claims headers without DTREK_DATE_TIME, ignores the distortion vectors; on a Saturn 944+ sweep that puts the spindle 90 degrees off (DIALS: 12% indexed vs 98% with the vectors applied, at the deposited cell). The arm geometry is confirmed by the data: the refined direct beam of a 2theta = 10 deg sweep lands at x = 621.1 against 621.6 predicted. The anomalous map peaks at 11.5 sigma on the two K+ and 6-7 sigma on S and P, so the hand is right. Battery, open arm: 5cc8 (rotating anode, Saturn 944+ SMV, 2theta = 10 deg sweep) and 9jq9 (Ga K-alpha liquid-metal jet, PILATUS3 1M miniCBF, single 450 deg sweep), both IRRMC. Run 20261001-2132_84228b_dtrek-home-source: 9jq9 passes (P 21 21 21, 1.65 A); 5cc8 merges to 1.53 A at the deposited cell but is called P 21 21 21 against the deposited P 21 21 2 (screw evidence on 00l 68-78 nats, tNCS at (1/2,1/2,0.11)) - left failing, not yet adjudicated. The Saturn gain (~5 ADU/photon) is not in the header and is not modelled. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>	2026-10-01 21:44:44 +02:00
leonarski_f	84228bf8be	v1.0.0-rc.173 (#83) ... * jfjoch_broker: Optional per-dataset authentication - statistics, images and plots can require a bearer token, which jfjoch_viewer supports. * jfjoch_viewer: Dark mode and a theme-matched colour scheme, a magnifier panel, and simpler contrast and background controls. * Rugnux: Multiple performance improvements on GPU and CPU (CPU-only processing up to 40% faster, faster image decoding on ARM), with unchanged results. * Rugnux: `--model` rigid-body refinement runs on the GPU, and the model-validation check is faster and more reliable. * Rugnux: Improved scaling and merging - error model, outlier rejection, absorption correction and French-Wilson amplitudes now agree more closely with XDS and ctruncate. * Rugnux: Improved integration - radial background on powder and ice rings, crowded rotation data keep their reflections, and CPU-only builds integrate large unit cells as GPU builds do. * Rugnux: More robust detector geometry - measured beam centre, X-ray bandwidth and goniometer rate, and geometry refinement accepted only on significant evidence. * Rugnux: Merged files are written in the standard setting, or in the setting of a reference MTZ, structure-factor mmCIF or model, with its free-R flags. * Rugnux: Richer report - ice and powder rings, further lattices, superstructure candidates and mosaicity, with warnings worded as prompts to check. * Rugnux: Clear error messages when a data set needs more GPU or host memory than is available. Reviewed-on: #83 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-29 15:57:32 +02:00
leonarski_f	6dfe065365	v1.0.0-rc.172 (#82) ... * Fixed `jfjoch_broker` cancelling every data collection with a CUDA "out of memory" error after long operation: GPU memory no longer leaks with each collection. * Rugnux scales a rotation sweep until the per-frame scales settle instead of for a fixed three rounds, and says so when they did not - merged intensities, and the space group, resolution cut and frame rejection read off them, change accordingly; `--scaling-iterations` is now the cap on that loop (default 100). * Rugnux places every frame of a marCCD, SMV or miniCBF series at the spindle angle its own header states, so a series with missing frames, or with angles written modulo 360, is no longer read at the wrong geometry or refused. * Every rotation run writes two diagnostic files beside its reflections: `<prefix>_detector.jpg`, the detector projection with the pixel mask and the detected beam-stop shadow drawn on it, and `<prefix>_plot.txt`, one row per image. Reviewed-on: #82 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-22 06:48:37 +02:00
leonarski_f	30b6800289	v1.0.0-rc.171 (#81) ... * Rugnux: basic support for CCD images (marCCD, SMV) and for gzipped miniCBF. * `jfjoch_viewer`: opens the CCD formats, and fixes to the dataset plots. * Documentation updates. Reviewed-on: #81 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-17 14:42:52 +02:00
leonarski_f	cb5a2f032a	v1.0.0-rc.170 (#80) ... * Fixed a `jfjoch_broker` crash during indexing: sorting no longer misbehaves on non-finite values, and GPU FFT indexer kernel launches are now error-checked. * rugnux needs about a third less peak memory to scale, merge and post-refine rotation data, with identical results. * `rugnux --model`: the placed coordinate file carries the space group its own coordinates obey, and says so when that is not the group the reflection files beside it carry. * `jfjoch_viewer`: fixes in the dataset plots, inspector and layout; spot markers lose their black outline by default (a checkbox under "Image features" restores it) and the highest-pixel markers are white boxes around the pixel. Reviewed-on: #80 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-16 18:17:46 +02:00