227 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	6081b6bc43	docs: credit the L test, FFT indexing, TORO, Niggli, peakfinder8 and SparseCCL ... Six methods the pages name or describe carried no citation: Padilla & Yeates (the L test), Steller, Bolotovsky & Rossmann (the projection/FFT autoindexing MOSFLM implements), TORO (what ffbidx implements), Krivy & Gruber and the ITA lattice-character table (the reduction and Bravais assignment), Cheetah's peakfinder8 (the per-ring background statistics of the adaptive finder) and Hennequin et al.'s SparseCCL (already credited to traccc, now also to its authors). Each gets its ACKNOWLEDGEMENT.md paragraph, a References entry in CPU_DATA_ANALYSIS.md, and a one-line credit at the algorithm. The Sheriff & Hendrickson / Popov & Bourenkov entry is re-scoped so each claim sits on the paper that supports it - P&B 2003 is titled, and credited for the sigma-aware anisotropy estimation its statistic modelling contains, not for the tensor and its constraints. All DOIs verified against the publishers; the SparseCCL DOI resolves to IEEE document 9049184 (IEEE blocks content scraping, so verified by the resolved document id plus two independent sources). Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:36 +02:00
leonarski_fandClaude Opus 5	86f8edfabc	docs: the FFT axis ceiling, one-sweep inputs, exit status and _anom.ccp4 ... The longest FFT axis (500 A, no flag; -C moves it) was implied twice and never stated, and its failure mode is a plausible sub-cell rather than a refusal. One input is one sweep - said affirmatively where inputs are described instead of in an aside about pointless. A default 50 A low-resolution cut discards real reflections on a very large cell; the option row says so. Exit status is documented for scripts (0 = completed, non-zero = stopped), and the --model output list gains _anom.ccp4, which was written but undocumented. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:36 +02:00
leonarski_fandClaude Opus 5	87b1402c50	docs: hand the output onward - downstream commands and the three blocking facts ... The page named phenix, REFMAC, POINTLESS, AIMLESS, careless and SHELXC a dozen times without one command line, and left unstated the three facts those programs stop on: the free-flag convention (0=work 1=free; REFMAC needs FREE 1), the phenix label choice the double intensity array forces, and the unmerged file's header symmetry and sort order (determined group, sorted H K L M/ISYM BATCH - WriteReflections.cpp sorts it). A new 'Taking the data onward' section carries the worked lines, the careless column renames (BGVAR is a variance), and the Phaser SGALTERNATIVE keywords for the enantiomorph the report leaves open. The POINTLESS series trap now names ALLOW OUTOFSEQUENCEFILES instead of telling users to touch their data, the report-grep block warns that SPACE_GROUP_NAME carries one member of an enantiomorphic pair by convention, and the P1 cross-check's free set is declared to be its own. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:36 +02:00
leonarski_fandClaude Opus 5	b1ae1ece67	docs: a default rotation run already writes real anomalous data ... The -A row and FRIEDELS_LAW=TRUE together read as 'without -A your Friedel pairs were averaged', which is false: the rotation merge always keeps the Bijvoet split and the default .mtz/.hkl carry it (WriteReflections.cpp, BuildMergedRows). Say what -A actually changes - the counting basis and the error model - and give the merged MTZ's exact column labels, which scripting against phenix needs. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:36 +02:00
leonarski_fandClaude Opus 5	40cb5cd6db	docs: the quick start tells the truth about inputs, outputs and the cutoff ... A default rotation run writes seven files, not five - the two the list omitted are most of the bytes. The input is any NXmx/EIGER master or miniCBF sweep, which the page said only 350 lines later after twice implying Jungfraujoch data only. The CC1/2-0.30 resolution trim moves up to the quick start, and _image.dat's columns are finally named (ScalingResult.cpp writes a # header). Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:36 +02:00
leonarski_fandClaude Opus 5	40403d7beb	docs: the direction grid bounds the longest findable axis; say so in 5.3 ... The ranking-not-sampling observation was measured on the coplanar-shortlist rescue and is scoped to it now. The angular-resolution bound theta < d_min/(2a) means the shipped 16384-direction grid resolves axes only to roughly 120-150 A, far below the 1200 A the accepted maximum admits, and the failure mode is a plausible sub-cell, not a refusal - the reader raising fft_max_unit_cell alone deserved to know it cannot work. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:36 +02:00
leonarski_fandClaude Opus 5	32adb882eb	docs: disambiguate the reused symbols and the bandwidth definition ... sigma_bw is one physical smear written in reciprocal units in 8.2/11.1 and in pixels in 9; the two Delta-phi of the partiality formula are named; 13.5's |s| = 1/d is reconciled with the s = sin(theta)/lambda of 10.6/14.2; bandwidth is the rms spread, with the FWHM-input conversion (/2.355, BraggIntegrationEngine.cpp) stated. The ice-extinction clause now covers (104), not only (00l), and the AIMLESS <I/sigma> = 2 constant is named as AIMLESS's default rather than pointed at a criterion this project does not use. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:36 +02:00
leonarski_fandClaude Opus 5	e94548c614	docs: the twinning exemption list, and why -1, 2/m and mmm are not on it ... The stated criterion (a merohedral twin law exists) formally exempts every holohedral Laue class, but the code (TwinningAnalysis.cpp) deliberately keeps the low-symmetry ones eligible because pseudo-merohedral twinning through a special metric cannot be excluded there. Say both halves, and give the reference values of the statistics so the mmCIF numbers can be read. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:36 +02:00
leonarski_fandClaude Opus 5	9814846ebd	docs: state the q convention at every numeric q and on the q flags ... Every q in the pipeline is 2*pi/d (Definitions.h, the azint bin mapping), but the numbers in 3.3, 7.6 and 10.10 and the --azim-* flags never said so, and a reader taking q = 1/d would set --azim-q-spacing or --azim-max-q wrong by 2*pi. The 7.6 ice triplet is spelled out so 'within 0.06 of one another' reads as the adjacent-ring spacing it is. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:36 +02:00
leonarski_fandClaude Opus 5	14b79b0314	docs: fix the sigma-ratio, the profile-fit term and the outlier cut as written ... The 1.109 in 9.2 is the variance ratio of the shipped 4/6/13 stencil (45/408 pixels), not the sigma ratio the sentence attached it to, and the effect is a bound attained on weak reflections, not uniform. The profile-fit background term is (sum P/v / sum P^2/v)^2 var(b), matching the code; the undefined w is gone. The 13.3 refit cut is N^2 times the model variance (RotationScaleMerge.cpp), not N*sigma^2. The sigma floor is 1 count. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:36 +02:00
leonarski_fandClaude Opus 5	f68fd3d7af	docs: pin the sign convention of the back-rotation in 7.3 ... R(phi) rotates the observations by +phi about the stored axis, which makes it the inverse of the crystal's own rotation - the reading under which the formula as written is correct, and the same convention that has the exported MTZ batch axis and the XDS echo negated. Said explicitly, so a reimplementation cannot take R(phi) for the crystal rotation and land at 2*phi. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:36 +02:00
leonarski_fandClaude Opus 5	694e687fce	docs: name the beam parameter as the PONI and state the laboratory frame ... Section 1.1 called (x_beam, y_beam) the direct-beam position while constructing it as the point of normal incidence; on a tilted detector the two differ by D*tan(tilt), and a reader loading a header direct beam into it would be wrong by several pixels. Name it as the PONI (the system-wide convention, DETECTOR_GEOMETRY.md), say which point the construction pins, and state the laboratory frame's axes and handedness, which the rotation-sign, R-centring and Bijvoet-hand discussions all silently depended on. Two-theta is computed as a two-argument arctangent; say so. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:36 +02:00
leonarski_fandClaude Opus 5	d3879d0112	docs: the change of hand is a label, only the ambiguity choice reindexes ... Both pages said in one place that adopting a model's enantiomorph moves no reflection, and in another that it is applied to the merged reflections and exchanges the Bijvoet mates. The code (ModelValidation.cpp, AdoptModelFrame) does the former: the model's group is a label on the written files, I(+)/I(-) stay as measured, and only the merohedral-ambiguity reindex touches reflection indices. Say that once, consistently, in CPU_DATA_ANALYSIS.md §14.5 and in the two RUGNUX.md passages that carried the wrong reading. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:36 +02:00
leonarski_fandClaude Opus 5	200a2d53b7	report: name the groups the data could not separate, as keys ... SPACE_GROUP_NAME is a scalar and reads like a determination, and the docs nominate a grep of it as the interface. Where several groups predict the same absences it is one of them, picked by convention: the report said so in prose and nothing machine-readable carried it, so a script recorded a coin flip as an answer. Refining against a deposited model in the wrong enantiomorph gives R = 0.549. Four keys, none of which change which group is adopted: the alternatives the data cannot separate; whether the enantiomorph was determined, given, or is undetermined - decidable from the group number alone, so it is answered even where the search did not run; and the higher point group whose promotion was refused, with its reason, which until now existed only as prose. REPORT_VERSION is 5. No existing key changed. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:22 +02:00
leonarski_fandClaude Opus 5	247130a841	-S: check the metric the fixed group needs, not only its centring ... Both guards on a user-fixed space group keyed on the centring differing, so an axis permutation within the same centring passed: a run that indexed a=37.909 b=78.031 c=77.594 and was told -S P41212 - which needs a=b with the 4-fold along c - merged through operators that do not act on its own indices, and --mode scale on it reported COMPLETENESS= 195.3, an arithmetically impossible number, without complaint. MetricViolation asks the setting-independent question instead: a group's rotations must leave the cell's metric tensor invariant. The re-seating arm now runs on either failure, so a permuted cell can be reindexed into the setting the group needs rather than merely refused; the refusal arm catches what re-seating could not fix. --mode scale never reaches either arm, so it gets the same test where it fixes its cell and its group, which is the only place an impossible completeness could still be produced. The tolerance is a refusal bound, so it sits above what a correct answer reaches: over 113 corpus runs every group determined from its own cell scores under 0.032 and the permuted case scores 0.764. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:22 +02:00
leonarski_fandClaude Opus 5	47ec939c39	merged MTZ: FreeR_flag in the convention its own column name carries ... The column was written with 1 for the test set and 0 for the working set - the phenix/CNS numbering - under FreeR_flag, which is CCP4's column name. CCP4's own freerflag writes 0..19 with 0 as the test bin, and REFMAC5's default FREE 0 reads it that way, so REFMAC5 stopped on every file we wrote: "more than half of reflections are in free R set", then "Cannot switch free R flag", exit 1. phenix auto-detects either numbering with equal confidence (measured on both, score 3 each), and rugnux's own reference-MTZ reader already takes flag 0 as the test set, so 0 = test is the numbering that works everywhere and the one the rest of the code assumes. This changes every merged .mtz we write: a script that reads FreeR_flag == 1 as the test set has to be inverted. The mmCIF's _refln.status_free is a separate item with its own convention and is unchanged. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:22 +02:00
leonarski_fandClaude Opus 5	762c093b10	unmerged MTZ: export the events the merge would keep, not every event ... The export declared its rows FULL - LDTYPE=2 in the batch header, M=0 in M/ISYM - while filtering them on --min-partiality alone (0.02), where the 3D combine also applies --min-captured-fraction (0.7 on rotation) to the same summed event. AIMLESS reads the FULL declaration, reports "all runs have only fulls" and ignores FRACTIONCALC, so an event that caught a twentieth of its rocking curve entered the merge whole, with a small sigma, and was weighted heavily. There was no cut for the reader to make: the column that would let it make one is the one the reading program has been told to ignore. Dropping those events moves AIMLESS's Rmerge at 1.8 A from 1.353 to 0.694 and CC(1/2) from 0.985 to 0.993. FRACTIONCALC itself is unchanged, values above 1 included. Each part's partiality is the erf pair the predictor computed on that frame, from that frame's own refined lattice and mosaicity, so the parts of one event do not tile the rocking curve exactly - the offset steps by the wedge to within 12% of it, and the sums land in a peak at 1.000 whose 95th percentile is 1.09. It is an honest estimate of a captured fraction, and it is not the number rugnux scales on, so clamping it would only hide the spread. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:22 +02:00
leonarski_fandClaude Opus 5	b33cae9068	unmerged MTZ: a batch header for every image the sweep spans ... The header set was built from the batches that produced an observation, so an image that indexed nothing left a hole in the phi series. AIMLESS starts a new run at such a discontinuity: measured on a 360 degree sweep with 67 unindexed images it made 23 runs of one sweep, its scale model diverged, Rmeas overflowed to -1266 and the result no longer correlated with rugnux's own merge (Pearson 0.0018). Renumbering the batches contiguously does not help - the split is on phi, not on numbering - so the fix is a header per image over the span the observations cover. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 09:18:22 +02:00
leonarski_fandClaude Opus 5	9c19646f6a	refine: fit the direction of the goniometer axis, not its length ... The residual applies angle_rad * |rot_vec| and rot_vec is a free three-vector, so the first pass has been fitting a goniometer rotation SCALE nobody asked for. GoniometerAxis::Axis() then normalises it away on write-back, and RotationIndexer scores the candidate with the normalised axis - so the cell that won the fit is judged under a rotation model the fit did not use. Measured over 43 rotation datasets: the length reaches 1.2%, and the fit-vs-score disagreement a median 0.124 deg and up to 6.19 deg of goniometer angle, against rocking widths of 0.05-0.36 deg. That score picks the lattice class, which nothing later revisits. The fitted length is not a usable measurement of anything either: on synthetic data it recovers 54% of a known scale error, repeated first passes on one dataset disagree with each other in sign, 26 of 43 datasets disagree with themselves, and on the one dataset with a proven 1.3% stage fault it comes out negative. It is absorbing other systematics. The rotation scale is measured properly, once, with cross-validation and gates, in PostRefine. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-01 18:36:32 +02:00
leonarski_f	d32c8d526b	geometry: make which tilt component is restrained two numbers rather than a shape ... Both directions of the tilt now go through the same restraint, with a budget each in shared direct-beam pixels; zero means free. Swapping which component is held, or holding both, is a change to two constants. The perpendicular budget is zero today, which is the arrangement the measurements support: it is the component whose conditioning tracks the 2theta the fit reaches, while the parallel one's does not move with 2theta at all - a conditioning number that ignores the data is the prior talking. This is a clarity change, not a precision one, and the record should not read otherwise: the standing 'freeing the tilt inflates both beam components' cost is the perpendicular component's doing, not the parallel one's, so restraining the parallel one recovers essentially none of it. What it buys is that a beam-centre error is no longer reported as an angle.	2026-09-01 15:34:06 +02:00
leonarski_fandClaude Opus 5	5869a27fe2	docs: one line per behaviour change in the rc.166 changelog, named by program ... The section had grown to eighteen entries, several of them describing the same report or carrying detail that belongs in a commit message. Consolidated to thirteen one-liners, each naming the program it concerns - rugnux, jfjoch_writer, jfjoch_broker, jfjoch_viewer - so a reader can find what changed in the part they use. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-01 15:20:40 +02:00
leonarski_fandClaude Opus 5	51e90f5549	report: say what the measured detector tilt is worth, and what it is not ... The report invited the reader to check REFINED_DETECTOR_TILT against a powder calibration. Measured over two detectors' worth of crystals, that check misleads: the rotation fit does one outer round, so it leaves its starting value by only a small and crystal-dependent fraction of the distance to the calibrated value, and on the worse of the two detectors the per-crystal median sits an order of magnitude further from the powder answer than either method's uncertainty. A user comparing one run against their own calibration would conclude the calibration was wrong. What survives the aliasing is the direct beam, which is already printed beside it, and the MEDIAN of the tilt over several crystals on one detector - enough to show up a placeholder or a stale value in the file, not enough to replace a calibration. Say that, and say not to feed one run's value back into the instrument. The conditioning law (VIF = 4.40 tan(2theta_95)^-1.66) was tested as a per-run gate and does NOT order the errors - the crystals whose fit stays put are found in the best-conditioned band as often as the worst - so no threshold is added here. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-01 15:15:01 +02:00
leonarski_fandClaude Opus 5	1a25d396a8	docs: the beam centre is the PONI, the direct beam is the beam ... Document direct_beam_x/direct_beam_y in the CBOR start-message table and in the HDF5 detectorSpecific catalogue, and add the section that says what the distinction is: the PONI is the foot of the perpendicular, the direct beam is where the beam lands, they are distance*tan(tilt)/pixel apart, and XDS ORGX/ORGY wants the second. Also record that the same field is a statement about the user's geometry in a broker master and a measurement in a rugnux _process.h5. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-01 15:15:00 +02:00
leonarski_fandClaude Opus 5	0e245d28cf	docs: name the in-house SLS 2.0 data beside the public sets ... The acknowledgement read as though the whole test corpus came from other people's beamlines. It does not - in-house data collected at SLS 2.0 is tested alongside it. One clause, at the top of the section; everything that follows still concerns the public data, which is the part that carries an obligation to cite. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-01 09:58:40 +02:00
leonarski_fandClaude Opus 5	8935a59721	rugnux: the two-pass guard says when it has no completeness, instead of printing 0.0% ... The guard that judges the post-refined pass against the header-geometry pass reads completeness off each pass's space-group search merge. That merge does not count possible reflections, so the quotient is 0.0 on both sides and every de-novo rotation report has been printing completeness 0.0% vs 0.0%, CC1/2 before corrections 0.994 vs 0.993 as though a comparison had happened. On the 28-dataset in-house battery that is all 28 runs. The number is not just uninformative, it is a test that did not run: "completeness above 100% means the cell is wrong" is the guard's wrong-cell arm, and it cannot fire against a constant zero, so only the CC1/2 arm decides - which is computed on whatever data the pass kept, so a pass that discards a large part of the sweep can post an equal CC1/2 and win. Carry a measured flag beside the number. The arm is skipped and the log and PASS_DECISION say "completeness not measured" where there is nothing to read. No behaviour changes: the arm could not fire before either. The next commit gives the merge the count so it can. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-01 09:48:25 +02:00
leonarski_fandClaude Opus 5	5ce7eb3014	docs: one changelog line for the geometry reporting work ... Three lines were appended over the course of the work - the tilt and direct beam in the report, the measured tilt beside them, and the post-refine beam bound. They are one change to a user: the report now describes one geometry and says which point is which, and the bound that governs it is measured against the run's own measurement rather than against the file it is meant to correct. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-01 07:39:23 +02:00
leonarski_fandClaude Opus 5	f98442077e	post-refine: bound the beam move on the measurement, not on the header ... PostRefine step B refuses a fitted beam centre more than 15 px from the geometry the run started from. Two things were wrong with that and they compounded. The 15 px was BOTH the Ceres search box and the acceptance threshold, so a fit that wanted to move further was pinned at the box face, landed at exactly hypot >= 15.0, and was then refused for being there. The gate never saw the fit it was judging. Measured on one crystal at three detector distances, the fit came back at 15.128, 15.133 and 15.130 px - the box corner, three times. And it was measured from the header, which is the value most worth correcting exactly when it is most wrong. The run already knows better: the default beam-centre check fits the centre from the isotropy of the scattered background on every rotation run, reported it, and then discarded it. The bound is now measured from whichever of the nominal centre and that measurement is nearer - accept a move that is small relative to something independent, rather than small relative to the header alone - and the search box is widened to match, so the gate decides rather than the box. The measurement is used only where it was precise enough to be adopted as a centre in its own right; a run without one is bounded exactly as before. Step B also now says WHICH of its four tests refused a fit, since all four leave the same geometry behind. Measured over 113 rotation datasets against the same corpus, one binary per arm, with a control arm that reproduced the stored battery on 112 of 112 reports: the bound fired and refused a real correction 1 6ukf the bound fired and caught a runaway 0 the bound never fired 112 On 6ukf the header centre is 22.1 px from what the background fit measures. The old fit, pinned at the box, improved the held-out positional residual 9-fold and was refused; the new fit lands 0.46 px from the measurement and improves it 418-fold. ISa 4.42 -> 6.71, R_meas 18.5 -> 12.8 %, CC1/2 0.987 -> 0.995, d_min 1.119 -> 0.973 A; at matched resolution, 1.68 A goes I/sigma 8.9 -> 15.1 and R_meas 28.8 -> 13.4 %. The refined cell moves from 0.4 % off the deposited one to under 0.1 %. It survives perturbation, and inverts it: over +-0.5 mm of detector distance the corrected run is flat (ISa 6.62 / 6.71 / 6.94) while the uncorrected one is bistable (4.02 / 4.42 / 6.90). The change removes an instability rather than exploiting one. No space group anywhere in the corpus moves, and no other dataset's report changes at all - 112 of 113 are identical. The distance half of the gate is untouched: it is separately argued, and it is what legitimately refuses the one dataset whose distance wants to move 1.05 %. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-08-31 20:19:36 +02:00
leonarski_fandClaude Opus 5	efca844bce	calibration: --no-refine-tilt holds the header tilt, it does not zero it ... GuessInitialGeometry resets rot1/rot2/rot3 to zero before seeding, and the branch that puts the header's tilt back was guarded by `refine_tilt && !tilt_refined`. With --no-refine-tilt the tilt is never free, so tilt_refined is false, so the guard is false, so the restore never ran - and the fit reported a zero tilt while the CLI printed "held at the header value". The guard only needs !tilt_refined: a tilt that was declined and a tilt nobody asked to refine both want the header put back and the beam centre and distance refitted around it. That is what the branch already does. Measured on a LaB6 sweep with a tilt imposed on the command line and asked to be held, --calibration spots: before Rot1= +0.0000 deg (+0.001400 rad from the header) after Rot1= -0.0802 deg (+0.000000 rad from the header) The rings path reaches this only when the spot-derived start wins, which is why it does not show on a file whose profile start is chosen; the spots path always did. A calibration whose header tilt is already zero is unaffected - checked, byte-equal distance either way. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-08-31 19:47:02 +02:00
leonarski_fandClaude Opus 5	dcfcff5bc4	report: the measured tilt, and one geometry instead of two ... Adds REFINED_DETECTOR_TILT - rot1/rot2 in degrees as rotation indexing measured them - so the value can be checked against a powder calibration, which measures the tilt from ring shape and is the better instrument for it. rot3 is not carried: a rotation about the beam is an exact null of a single-axis rotation experiment, so the fit cannot move it and printing it would suggest otherwise. Also repairs two defects in the commit that added DETECTOR_TILT, found in review. The geometry was taken from the caller's copy of the experiment, which is the state BEFORE the run, while BEAM_CENTRE and DETECTOR_DISTANCE come from result.used_*, which is the state after - so on a rotation two-pass the report mixed a post-refined centre with the file's rotations and DIRECT_BEAM was off by the whole post-refinement shift. JFJOCH_DATASET_SETTINGS carried the same mixture, which is a geometry no pass ever ran at. The tilt and the direct beam are now taken from experiment_ alongside the other three, so the block describes one geometry. And the prose claimed the tilt "is not refined here". It is: rotation indexing refines rot1/rot2 on every rotation run. What is true is that the result is never written back onto the geometry, which is why it needs a key of its own. M_PI -> PI (common/JFJochMath.h). rugnux is in the forced-Windows viewer-only set and M_PI is not portable to MSVC; the file did not include <cmath> either. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-08-31 19:35:27 +02:00
leonarski_fandClaude Opus 5	7c00731992	docs: publish the powder calibration schemas in the python client docs ... docs/python_client is tracked and is what readthedocs publishes, but it is generated - update_version.sh copies it out of python-client after regenerating the client - so adding schemas to the spec left it four files behind. The README's model list did not name them and their pages did not exist. Copied the way update_version.sh copies them. The four new pages and four lines in the README, nothing else: the generator's README is built from the spec, so the stale Calibration* pages it had left on disk under the old names are absent from it and were removed before copying rather than published alongside their replacements. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01NfuDvf5ipV3Hi8TiCUKD27	2026-08-31 19:02:12 +02:00
leonarski_fandClaude Opus 5	8691bf4876	calibration: write the result as JSON, not only as a PONI file ... A calibration run produced one file, and it was a pyFAI PONI - which pyFAI and its neighbours read and nothing in this system does. Carrying the answer back into the instrument meant a person reading numbers off a printed report and retyping them into a dataset_settings body, and the report is where the two points a "beam centre" can mean are easiest to confuse. So write <prefix>.json beside it. Its "dataset_settings" member holds the geometry under the property names broker/jfjoch_api.yaml gives them and holds nothing else, so it is a valid dataset_settings body as it stands: curl -X POST -H 'Content-Type: application/json' \ -d "$(jq -c .dataset_settings det.json)" http://broker:5232/start beam_x_pxl is the PONI, as everywhere here. The three poni_rot*_rad ride along whenever any is non-zero and are left out when all are zero: a body without them does not leave the tilt unstated, it states a FLAT detector, so they travel together or not at all - the same rule the report's JFJOCH_DATASET_SETTINGS block already follows. The "calibration" member holds what the run knows about that geometry: the residual, the fit's own sigmas and the correlation between the tilt and the beam centre, whether the tilt cleared its significance test or was declined and pinned, where the direct beam lands, and where the spots independently put the beam. A calibration that has gone wrong looks exactly like one that has not until those are read, and a machine-readable file that carried only the geometry would be the easiest possible way to feed a bad one into an instrument. Tested against the model generated from the spec rather than against a list of field names written out by hand: the file's dataset_settings member is parsed into org::openapitools::server::model::Dataset_settings and validated, so a field renamed or newly required in jfjoch_api.yaml fails here rather than at someone's POST. The tilted and untilted branches are both covered, and the PONI/direct-beam distinction is asserted rather than assumed. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01NfuDvf5ipV3Hi8TiCUKD27	2026-08-31 18:47:51 +02:00
leonarski_fandClaude Opus 5	9267bd67de	report: the detector tilt, and the two points the beam centre is not ... BEAM_CENTRE is the PONI - the foot of the perpendicular from the sample - so on a tilted detector it is not where the direct beam lands. The report printed only that one number and never mentioned the tilt at all, so the two points were indistinguishable to a reader. On a detector at 85 mm with a 0.22 degree tilt they are 8.3 px apart. Print DETECTOR_TILT (rot1/rot2/rot3, degrees, as the run used them - nothing is refined here) and DIRECT_BEAM beside BEAM_CENTRE, and say which is which. JFJOCH_DATASET_SETTINGS was the more serious half: it exists to carry a geometry back into the instrument, and dataset_settings carries poni_rot1/2/3_rad, but the block omitted them - so it described a FLAT detector, silently, on every tilted setup. The rotations now ride with it when they are non-zero; they stay out when they are zero, because the API's own default is 0.0 and the shorter block means the same thing. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-08-31 17:35:03 +02:00
leonarski_fandClaude Opus 5	ba24946c0f	twinning: do not report a twin the L-test rules out ... The two indicators can only move one way under twinning - <|L|> down from 0.500 toward 0.375, the second moment down from 2.0 toward 1.5 - but they were combined with an OR, so a narrow intensity distribution could report a twin on its own while the L-test said the opposite. That is not a marginal disagreement. It fires on small-cell rotation data, where a twin fraction of 0.50 was reported for a crystal whose <|L|> was 0.63: a value no twin can produce, and one that points at the opposite situation - a structure whose intensities behave centric. Suppress the flag when <|L|> sits at or above its untwinned value; the two indicators are otherwise combined exactly as before. Measured over 113 stored reports: two flip, both of them wrong today, and nothing else moves. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-08-31 15:34:16 +02:00
leonarski_fandClaude Opus 5	71cca91ec1	rugnux: rank screw candidates without the control count ... A screw's control class is the complement of its absent class on one axial row, so the two move together: a candidate that predicts more of the row absent leaves fewer reflections to be judged against. The Beta tail AbsenceEvidence computes grows with that control count, so the stricter candidate was charged for the very reflections it correctly called extinct, and a group whose predicted-absent class is a strict superset of another's - with the extra reflections equally dead - could score LOWER than the group that explains only part of the row. Two mechanisms, one dataset each. * The control-count minimum gated the row MEAN, which is the scale the zone's evidence is stated in, on the same count as the row MEDIAN, which is a violation threshold. A candidate could therefore forfeit a whole zone by being right: on a tetragonal 4_1/4_3 wedge, thirteen 00l reflections measured at 0.1% of the two l = 4n beside them scored ZERO because only two control reflections were left, while the nine of them a 4_2 also predicts absent scored 38.7. The mean now stands on two, the median still on three. * The Beta tail is replaced, for a SCREW zone only, by its b -> infinity limit - the same statistic with the control count dropped. A p-value computed against each candidate's own null is not one scale across candidates; what is left is the likelihood ratio of the absent class against Wilson at the row's own mean, which is a sum over reflections and therefore comparable. Asymptotically it is n_absent * (log(1/ubar) - 1), so an equally dead superset can no longer score lower. Measured on a tetragonal 4_1/4_3 crystal: 29 dead 00l against 8 control read 47.7 nats where a subset of 19 of them against 18 control read 55.5. The centring statistic is untouched: its control is the whole present population, not the complement of a claim on one row, so neither mechanism applies to it. Measured. Analytic superset monotonicity, on a 176368-point grid with no calibration and no corpus: 1.29% violations -> 0.00%, exactly monotone wherever both candidates keep a control class. Over 112 stored merges (open, in-house and private arms) exactly ONE decision changes and it is a gain, a 4_2 -> 4_1/4_3 swap on a deposited 4_3; the screw column over the deposited arm goes 33/41 -> 34/41 with zero screw over-calls before and after, and the four centring outcomes are bit-identical. An eight-wedge reproducer whose 00l row a strict candidate eats goes from two mis-calls to none, end to end. The refused side moves the safe way: 103 zones the old statistic scored negative go lower, none turns positive, and the minimum evidence of an adopted screw rises 20.4 -> 23.8 against an unchanged bound of 20. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-08-31 15:33:29 +02:00
leonarski_fandClaude Opus 5	c25418319a	report: the twinning measured before the search, and the strong-direction limit ... Three additions to the report, none of which changes a number the run computes. The twinning statistics printed today are measured in the Laue class the run ADOPTED, so where the search promoted the point group they can say no more than "no twin law exists inside the class it chose" - and a twin is precisely what would have caused that promotion. The uncontaminated pair was already computed on the subgroup merge the search was given and reached only a log line; it is now printed as L_TEST_MEAN_ABS_L_BEFORE_SEARCH and SECOND_MOMENT_I_BEFORE_SEARCH, beside the post-adoption pair rather than instead of it, since the two answer different questions. ANISOTROPY_D_MIN_BEST names the finest of the three principal limits so it can be grepped, and a paragraph distinguishes the three resolutions the report now carries: what was written, where the isotropic fit crossed, and how far the crystal reaches where it reaches furthest. It is read off the fitted tensor rather than off the cut, so it can land either side of the other two - measured on one dataset at 2.01 A against a 1.81 A cut - and the text points at ANISOTROPY_D_MIN_CENSORED for when it is the edge of the data instead. A warning when CC1/2 falls and then climbs again, which means the fall-off the cut is read off does not describe the data. A climb counts only above CC1/2 0.30 and only if it exceeds 0.05: past that the number is oscillating in noise beyond any cut this run would take. It advises no re-cut - the generous cut is deliberate. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-08-31 14:06:42 +02:00
leonarski_fandClaude Opus 5	d189faeec7	viewer: draw grid scan cells in the proportion of the scan steps ... A grid scan with, say, a 20 um step in x and a 5 um step in y was drawn as a square grid, so the picture had nothing to do with the shape of the area that was scanned. The cells now carry that proportion. The anisotropy lives only in the view transform: JFJochImage gains a pixel_aspect_ (the drawn height of one pixel in units of its width, 1.0 for a detector image), the initial fit fits the image as if it were that much taller and then puts the factor back into the transform, and the grid view sets it from |step_y / step_x|. Scene coordinates stay one unit per cell, so the mouse mapping, the selected-image box, the pixel labels and the ROI code need no change and the uniform wheel zoom keeps the proportion. Measured on an 8x4 grid driven offscreen: m11/m22 comes out 4.000 for steps 20/5 um, 0.250 for 5/20, 12.333 for 37/3 and exactly 1.000 - the old behaviour - for a square step. Every cell centre still maps back through mapToScene to its own cell in all four cases. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Hcoh6VNrmSswjfeMeDQqWP	2026-08-31 13:38:51 +02:00
leonarski_fandClaude Opus 5	756c3a22bb	docs: confirmed cells for three small-molecule sets; drop the unprocessable CCD one ... The four Diamond I19 small-molecule datasets had no reference of any kind, so a run on them could not be scored at all. Three now have one, each from a published structure with its DOI verified against Crossref; the fourth has a published space group but no numeric cell anywhere, which is recorded as such. Also removes the "obtained but not in the table" section. That dataset is stored as CCD TIFFs the reader does not support, so it is not processed here and adds nothing to a page about what the test corpus contains. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-08-31 11:02:38 +02:00
leonarski_fandClaude Opus 5	6d37b31948	report: give the resolution the CC1/2 fit reached, not only the one it was cut at ... The automatic cutoff fits the CC1/2 fall-off, takes the crossing of the target (0.30 by default) and then deliberately keeps one more shell. Only the extended limit was reported, as INCLUDE_RESOLUTION_RANGE, and that is the number a reader takes for "the resolution of this dataset" - so the report quoted a limit that is generous on purpose as if it were the measurement. The generosity itself is right and stays: a shell that is included can still be downweighted or dropped by refinement, while one that was truncated cannot be put back. What was missing is the other number. ComputeCCHalfLogisticCutoff now also returns the crossing, ApplyResolutionCutoff passes it out, and the report prints it as FITTED_RESOLUTION beside the range the reflections were written to, with a sentence saying which is which. The log line names both as well. Nothing about the cut, the merge or the written reflections changes. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-08-31 11:02:37 +02:00
leonarski_fandClaude Opus 5	55d9e2536f	release: 1.0.0-rc.166 ... The changelog entry for this release is six lines, not the fifty-four the development log had accumulated: what a user of rc.166 gets is native miniCBF input, masters from other facilities opening, the beam centre measured on every run, a 2theta-swung detector placed where the file says, the unmerged MTZ and a P1 merge written by default, and a substantially reworked symmetry determination. The per-change detail is in the commits. update_version.sh regenerates the three clients from broker/jfjoch_api.yaml, so this also carries the one API description that had drifted from the generated code - fft_high_resolution_A, which sizes the FFT's projection histogram and does not filter spots by resolution. Everything else in the regenerated tree is the version string. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-08-31 09:11:22 +02:00
leonarski_fandClaude Opus 5	3a30dc8ab5	rugnux: a space group that names twice the cell is a signal to halve it ... C 1 1 2 and C 1 1 2_1 are the only two monoclinic settings whose change of basis from the reference has determinant 1/2, and the reason is physical: with unique axis c the C-centring vector lies wholly in the oblique a-b plane and reduces away. Such a group is never a distinct Bravais centring - it is a primitive lattice written on twice the cell - and it wins the candidate table only because the table is scored on that doubled cell, where half the reflection positions are absent by construction. Refusing to enumerate those settings was measured and is worse: the volume-preserving alternative keeps the by-construction absences as real observations and merges no better than P1. So keep the enumeration as it is and act on the win instead: halve the cell, re-classify in the group's own system, carry the reflections across (the invented positions map to non-integral indices and are dropped, which is what the centred candidate was already doing) and search again there. Measured on one rotation crystal: C 1 1 2_1 on 68.6 73.0 170.3 90 90 90 becomes P 1 2_1 1 on 50.1 170.3 50.1 90 93.5 90, exactly the deposited setting, with every merge statistic unchanged (R_meas 0.1209, CC1/2 0.9979, d_min 1.238) and ISa 18.27 -> 18.31. Stable across +/-0.5 mm of detector distance. Eight other crystals are bit-identical, and across 112 stored battery reports exactly one adopts a volume-doubling setting. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-08-31 07:19:38 +02:00
leonarski_fandClaude Opus 5	7c3ab72fed	reader: refuse a CBF that is not a detector image instead of misreading it ... Three ways a miniCBF opened silently wrong. A byte-offset CBF with no PILATUS header at all was accepted: Count_cutoff then defaulted to 0, SaturationLimitFromValue(0) is 1, and every pixel at or above one count was flagged saturated - the integration accept gate drops the whole reflection, so the run comes out empty for a reason nothing reports. The pixel size defaulted to 0 with no validation anywhere downstream, which collapses every resolution, every scattering vector and the beam centre in millimetres. XDS writes its correction files in exactly this shape, so this is not hypothetical. A pixel size is now required to claim the file at all, and a missing Count_cutoff leaves the saturation limit unset - falling back to the container's own overflow, which can only fail to call a pixel saturated - with a warning saying so. And the header captures are character classes, not number grammars: "[\d.eE+-]+" matches a bare "." and "(\d+)" matches a digit string too long for int64. std::stod and std::stoll answer both with a raw std:: exception, which escaped the format probe - CanRead catches JFJochException only - so merely LOOKING at a corrupt file threw out of the viewer's open path. A header field that does not parse is now reported as a malformed header. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-08-31 07:17:40 +02:00
leonarski_f	e0ff51e2a0	lattice: transpose the change of basis to a primitive cell, as everywhere else ... gemmi states centred_to_primitive as an operator on COORDINATES and CrystalLattice::Multiply combines BASIS VECTORS, so the matrix has to be transposed on the way in - as it already is at both of the other places a gemmi Op::Rot reaches Multiply, one of them in this same file. A, B, C, I and F are symmetric matrices, so for them the transpose is a no-op and the omission never showed. R and H are not. Measured on an R-centred hexagonal lattice, ToPrimitive('R') returned 59.5 81.7 43.3 / 145.6 124.5 46.7 where the rhombohedral primitive cell is 49.3 49.3 49.3 / 60.9 60.9 60.9. What hid it is that a determinant is unchanged by transposition, so the VOLUME came out right - and most callers only take the volume. It is not only cosmetic: the result feeds the re-seating path that puts a lattice into a space group the user fixed by hand, so an R-centred lattice was handed the classifier a "primitive" cell that is not that lattice - broken for exactly the centring whose setting most needs re-seating. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N (cherry picked from commit 6ca00e927d664e870515c04164defa81d8a18725)	2026-08-31 07:17:00 +02:00
leonarski_f	527a5187f4	lattice: restore the character that names a centred monoclinic mI reduced form ... ITA character 43 was absent from the table. It is the type-II reduced form of a centred monoclinic lattice with no length equality - mC, mI, mA and mF are one Bravais lattice in four settings, and this row names the one whose conventional cell comes out I-centred. With the row missing such a cell reaches character 44 and is reported as triclinic, losing its centring outright. It accounted for 30 of the 31 demotions left after the two fixes before this one, and for 4.1% of random centred-monoclinic lattices. Both of its conditions are equalities on scalar products - International Tables gives them as 2|D+E+F| = A+B and |2D+F| = B - so the three angle tests are vacuous for it and the second equality is what selects it. cond_2DF was declared in the character struct and never tested against anything, because until now no row used it. Audited over 14000 exact lattices, the row fires 35 times: 32 are centred monoclinic lattices it recovers correctly and 3 are triclinic cells it promotes, all three of which Le Page promotes at the same tolerance. No over-call is attributable to it. The row is taken from International Tables rather than derived - no single integer matrix of determinant 2 covers more than 68% of these cells - and the test checks the conventional cell it produces has two right angles and twice the primitive volume. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N (cherry picked from commit 4c2baf0cc3b2177196a9448df06e24b5446de96a)	2026-08-31 07:17:00 +02:00
leonarski_f	931d7acc7c	lattice: judge a structurally-zero scalar product against the size of the cell ... The Niggli type of a reduced cell is the sign of its three scalar products, and gemmi's reduction was asked to decide those signs against an absolute tolerance of 1e-9 while the products themselves are 10^3 to 10^5 A^2 and the cell is held in float. A product that is structurally zero therefore arrives carrying about 1e-4 A^2 of rounding and is read as definitely signed. The reduction lands on the wrong side of the type-I/type-II boundary, the character written for the other side matches nothing, and the lattice comes back with less symmetry than it has. It is not a corner case. Take an exactly body-centred tetragonal lattice with c > a*sqrt(2) and merely ROTATE IT IN SPACE: 38 of 60 rotations lose the 4-fold, and it comes back C-centred. Every lattice this code classifies is a refined, rotated one; the two tetragonal-I cases already in the tests are axis-aligned, which is the one corner where the rounding vanishes. The tolerance is now scaled by the cell's own magnitude. Over 14845 exact lattices that puts it on a plateau three decades wide - demotions 461 -> 31 - with the over-call count unchanged at every point of it, and with the three fixes that follow the plateau is four decades wide and the demotions are zero. The constant is 100x the one Grosse-Kunstleve et al. give because theirs is calibrated for a double-precision cell and this one is float: measured, their value recovers 6% of these lattices and this one 93%. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N (cherry picked from commit b82f217719450e1e46e94be5b5a43ed8ffbf2ca4)	2026-08-31 07:17:00 +02:00
leonarski_fandClaude Opus 5	b31fb0a55c	symmetry: take the point group from whichever merge found it, the absences from all observations ... The search runs on two merges - one holding every observation, one holding only the well-measured ones - and the second was allowed to report but never to decide. That cost real symmetry: over the corpus the two arms disagree on eight crystals and the arm that found the LARGER point group is right on all eight. A promotion is refused by the most damning statistic it can be shown, so only one of the two arms has to be starved for a genuine operator to be thrown away, and which arm that is depends on the crystal. But the two halves of the answer do not come from the same place. Absences live in the weak reflections the filter discards, so adopting the filtered arm whole recovers the point group and loses the screw - a P6_5 crystal comes back as P6. So the arms are split rather than ranked: the point group is taken from whichever supports the larger one, and its absences are then judged here, on every observation. SearchSpaceGroupOptions::fixed_point_group was written for exactly this and had no caller. Measured on the deposited arm: a trigonal-3 answer becomes P 6_1 against a deposited P 6_5 (an enantiomorph pair, so correct), and a monoclinic answer becomes P 2 2 2 against a deposited P 2_1 2_1 2. The screw survives the split, which it did not when the filtered arm was adopted whole. No crystal that was already right moved, and the over-call column is unchanged. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-08-31 07:17:00 +02:00
leonarski_fandClaude Opus 5	d35e8f680f	symmetry: say when the cell metric hosts more symmetry than the group adopted ... Every symmetry under-call in the corpus has the same signature: a lattice whose metric carries rotations the adopted group does not, with nothing in the run saying so. The user is left to notice that a P1 answer sits on a cell whose axes are equal and whose angles are 60 degrees. So a run that determines its own group now compares the two and says what it sees. It decides nothing - no threshold, no promotion, no demotion, no reprocessing - and the message says as much, because a pseudo-symmetric metric is ordinary and only the intensities can settle whether the extra rotations are real. Measured over 83 crystals it fires on 19 and covers 6 of the 7 point-group under-calls; on the crystal whose deposited group is F 4 3 2 and which rugnux reports as P 1, the line reads "the cell metric is cubic - it admits 24 rotations where P 1 has 1". The metric symmetry is Le Page's, taken through GEMMI's implementation, at an obliquity of 1 degree - the middle of the band over which the answer is stable. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-08-31 07:17:00 +02:00
leonarski_fandClaude Opus 5	493be2cf19	symmetry: enumerate the settings the cell can host, not only the reference ones ... The space-group search offered a candidate only if gemmi calls it the reference setting. A setting is a statement about direction, so that restricted the search to the axes the convention chose: a crystal whose 2-fold lies on c had no rung between P1 and 222 and fell to P1, and one whose screws lie on b and c was reported as the group with a single screw on c - the wrong group, not a lower one, because the candidate that predicts a subset of the real absences and nothing else wins on no evidence at all. Both stages now enumerate more, under refusals rather than thresholds. Stage B offers the non-reference settings of the chosen point group. Their rotation set is equal to the chosen one, not merely contained in it, so this cannot raise the symmetry; what it adds is a screw or a centring on the axis the data show it on. A candidate is offered only if the cell's own metric admits the rotations its setting names, and one predicting exactly the absences another candidate already predicts is dropped as the same hypothesis under a second name. A non-reference candidate whose centring class this merge does not contain is refused outright: the reference path may adopt an untested centring because the caller's centred-lattice re-test backs it, and a non-reference setting has no such backing. Stage A offers the rotation sets no reference setting carries - the a-unique and c-unique monoclinic 2-folds, and the two rhombohedral-axes trigonal groups - and only those, so every point group reachable before is still reached by the same group in the same setting. A rung reached only that way may be ADOPTED but does not judge anything else: it is skipped when the reference chi^2 is formed and when a higher promotion's parents are collected. Without that it made higher promotions strictly harder - a promotion answers to the most damning of its parents, and offering two more order-2 subgroups of 222 refused 222 and 432 on crystals that had them. The run report gains SPACE_GROUP_NAME beside SPACE_GROUP_NUMBER, since the number alone does not say which axes a group's symmetry lies on, and a group that is not a reference setting is printed as its extended Hermann-Mauguin name. The two-arm reconciliation compares point groups by that name rather than by number for the same reason. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01T3yNBXk4wKdMZy1ak2NY7f	2026-08-31 07:17:00 +02:00
leonarski_fandClaude Opus 5	26fc4b02b3	symmetry: carry the space group as the group, not as its number ... The adopted space group travelled the pipeline as a bare int and was rebuilt downstream with find_spacegroup_by_number, which returns the reference setting. So every setting a number cannot name was destroyed one line after it was determined: P 1 1 2 came back as P 1 2 1, I 1 1 2 as C 1 2 1, R 3:R as R 3:H. DatasetSettings now holds the gemmi::SpaceGroup itself, DiffractionExperiment exposes it as GetGemmiSpaceGroup() / GetSpaceGroupOrP1(), and everything that used to take an int - HKLKeyGenerator (its int constructor is gone, so the compiler finds the callers), the merge, the R-free flags, French-Wilson, the reindexing ambiguity, the completeness enumeration, the MTZ and mmCIF exports, the model validation - takes the group. -S keeps the setting the symbol names rather than reducing it to a number. The end message carries both spellings and a reader prefers the name, since only the name keeps the setting while the number is what a reader written before the name understands. It carries them over CBOR too: the determined group was never serialised at all, so a group rugnux chose reached the master file only when the same process wrote it, and an online writer fell back to whatever the user had supplied at the start. Both keys are optional additions, so an older reader skips them and a newer one reads an older sender. On disk the master's /entry/sample/space_group carries the extended Hermann-Mauguin name and is what the reader takes the group from, so a setting survives a _process.h5 and the --mode scale that re-reads it; the number stays beside it and is the fallback for files written before. Every one of the 230 reference settings the old writer could produce reads back as itself, so older files are unaffected. Stage A and Stage B of the search still enumerate reference settings only, so this determines no group differently today - it is what the enumeration needs before it can be widened. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-08-31 07:16:43 +02:00
leonarski_f	6ed4ea541e	reader: a link to a file that is not there is not a dataset that exists ... Every DECTRIS Eiger master links saturation_value, pixel_mask, bit_depth_readout and serial_number into a companion <prefix>_meta.h5, and that file is routinely not kept when a dataset is archived or deposited. The existence test asked only whether the LINK was written, which it is, so every optional-field guard in the reader answered yes and the read that followed threw. A deposited Eiger 16M set could not be opened at all, over values the reader was perfectly prepared to do without. Exists() now asks the second question too - whether the object the link names can be reached - so an orphaned link reads as absent and the fallbacks behind it do their job. The saturation value is then allowed to be missing outright, because on such a file it is: neither the NXmx name nor the DECTRIS one is readable, and there is no third place to look. Left unset, GetSaturationLimit() falls back to the container's own overflow. That is the safe direction - it can only fail to call a pixel saturated, where too LOW a value drops the whole reflection and silently removes the strongest data - and the run says out loud that nothing will be called saturated. The set that could not be opened now processes to 2.17 A against a deposited 2.40 A, in the deposited space group, with a cell agreeing to 0.08%. Output is byte-identical on datasets that already opened. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N (cherry picked from commit 0637979f6d95b446406ab70d1f3982841d195b36)	2026-08-30 21:43:54 +02:00
leonarski_fandClaude Opus 5	fb18457e6f	docs: bring the changelog and the method notes up to rc.166 ... The rc.166 changelog was missing fourteen user-visible changes and carried rationale and measurements that belong here instead. Added: the native miniCBF sweep reader, the third-party and firmware-1.x NXmx masters, the plain LZ4 filter, the image orientation taken from the file's module direction vectors, the two beam-centre flags and their rescues, and the FFT reach past 500 A. Trimmed the rest to one line each, moving the numbers out of the user-facing file. RUGNUX.md described the input as a single Jungfraujoch master file, which it has not been since this branch; it now covers the foreign and legacy masters, the accepted compression filters and the miniCBF sweep, including how a sweep is collected from one named frame. Six options existed with no entry in the table - --beam-center-check, --beam-center-search, --fft-min-unit-cell, --min-indexed-spots, --rot3 and --no-p1-crosscheck - and -C now moves both FFT cell bounds, which was not written down anywhere. CPU_DATA_ANALYSIS.md carried two statements this branch made false: 7.5 still said pass 2 reuses pass 1's space group, and 13.1 still said centrings are ranked by net absence count. Both now describe what the code does - the group is determined after pass 2, and centrings are ranked by the same Beta-tail likelihood the screw test uses. Also documents the per-zone screw scoring, the coplanarity volume-fraction guard, the plane-normal transform, the FFT cell bounds and the twelve refined candidates. The miniCBF reader implements the x-CBF_BYTE_OFFSET scheme and reads the imgCIF axis table from the specification alone. No CBF code is vendored or linked, so there is no licence obligation, but reimplementing a published specification carries one of credit: ACKNOWLEDGEMENT.md gains a section and the two algorithms carry a one-line reference each. Both DOIs were resolved before being written. Rottger's initial was wrong where this branch first cited it - K, not A. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01MxrrPcxodNiXzhNiECCVp5	2026-08-30 21:15:31 +02:00