22 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	e9da892790	Rugnux report: low warning thresholds, worded as prompts to check; ice apart from powder ... Owner decision: a warning is a prompt to check and must catch the real cases (9min) at the cost of some spurious ones. The physically motivated corrections stay (<|L|> outside its physical range is not twinning; a single sweep's indexing choice; NO_LATTICE on rotation; the no-crystal report); thresholds raised only to cut noise come back down: - SUPERCELL_POSSIBLE warns wherever the class measures and rocks (as before rc173's audit fix), worded as "check the cell", naming weak ordered intensity of a correct cell and spots of further lattice domains as the other readings. 9min (rock 4.2%) warns again. - LATTICE_TRANSLATION warns on every admitted vector (>=75% of the origin); below 90% the wording names a very strong pseudo-translation as the other reading. - PSEUDO_TRANSLATION warns on every detection; below a 20% peak it is worded as weak, check. - SWEEP_GAPS warns where the degraded ranges cover at least 1% of the sweep (the 4 sets of 77 below that had 1-2 frames, 0.4-0.6% of the sweep). - Powder rings are split between hexagonal-ice positions and the rest (MeasurePowderRings, report-only fields); ICE_RINGS and POWDER_RINGS warn separately from 5% of the spots, and ICE_RINGS also where the merge's ice gate found ice. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C	2026-09-26 14:02:05 +02:00
leonarski_fandClaude Opus 5.5	8a8c992cca	Rugnux report: warn only where the evidence supports the claim ... Report-layer fixes from the warnings audit of the rc173 full battery. Processing is unchanged (merged MTZ/HKL bit-identical on the sets checked). - SUPERCELL_POSSIBLE stays a key and a summary line; a warning only where the rocking part reaches 20% (sub-cells that refine normally rocked at 2.1-16.2%, the accepted doubled cells at 4.2% and 29.1%). The summary says where further lattice domains may put spots on the half-integer nodes. - LATTICE_TRANSLATION only where the Patterson at the vector reaches 90% of the origin (UNDECLARED_LATTICE_TRANSLATION_PCT, new); the two admitted vectors on the battery read 79% and 85% on crystals refining in the deposited cell, and are now reported as a very strong pseudo-translation. PSEUDO_TRANSLATION warns from a 20% peak (xtriage convention; detected peaks were 8.1% on one set, 24.8-63.2% on the rest). - <|L|> outside 0.375-0.55 (on the adopted or the pre-search merge) is TWINNING_VERDICT= NOT_READABLE with no warning, instead of a twin or SYMMETRY_SUSPECT reading. - NO_LATTICE no longer fires on a rotation run that indexed the sweep with no frame indexed on its own; INDEXING_RATE is --developer on rotation. - A rotation run that finds no lattice writes a report (VERDICT= FAILED, NO_LATTICE) before exiting 1, instead of an input-parameter error and no report (NoLatticeFound). - Powder and Ice summary lines, ICE_* keys, and a POWDER_RINGS flag from a 0.5 spot fraction. - SWEEP_GAPS warns only where the degraded ranges cover 10% of the sweep (77 -> 48 sets). - A single rotation sweep no longer carries an INDEXING_AMBIGUITY warning (one orientation matrix, consistent hand); INDEXING_AMBIGUITY_OPERATORS and an Indexing choice line instead. - A DOMAIN more than 10 deg away is a second crystal; the MULTIPLE_LATTICES sum is documented. - Mosaicity line and docs name XDS's suggested REFLECTING_RANGE_E.S.D. as the comparable number (0.90x median over 34 in-house sets; per-image SIGMAR runs ~1.35x higher). - HARMONIC_CONTAMINATION, SCALING_NOT_CONVERGED, POWDER_RINGS in the documented vocabulary. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C	2026-09-26 14:02:05 +02:00
leonarski_fandClaude Opus 5.5	a0518abe62	Rugnux: warn about further lattices only where they are domains of the crystal ... MULTIPLE_LATTICES and EXTRA_LATTICE_INTENSITY_PCT now count DOMAIN, TWIN_DOMAIN and SEGMENTED lattices only. A FOREIGN lattice (an unrelated cell) is still listed but no longer warned about: it is as often a wrong main lattice or tNCS as a second crystal (one of the four such sets in the battery census is a tNCS crystal). On the census this names 25 of 200 rotation sets instead of 29. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C	2026-09-25 21:32:14 +02:00
leonarski_fandClaude Opus 5.5	ddf718f91b	Rugnux: report further lattices in the leftover spots, and the mosaicity ... Rotation, report only: once the first pass has its lattice, the spots it leaves over (ice left out) are indexed again with a fresh rotation indexer, up to three times. A lattice is kept when the leftover validation spots sit on it far more often than at a displaced spindle angle (z >= 5, the first pass's own null), and classified against the main lattice: a misoriented domain of the same cell (split crystal), one turned by 180 deg (non-merohedral twin domain), one concentrated in part of the sweep (>= 60% of its spots in 2 of 8 blocks), a related cell (volume n or 1/n) or an unrelated one. Misorientation is the minimum over the bases whose metric matches, so a lattice symmetry is not read as one. EXTRA_LATTICE_* keys, a summary row, and a MULTIPLE_LATTICES warning where domains or an unrelated lattice hold >= 10% of the non-ice spot intensity (29 of 200 battery sets in the exploration census). Its own IndexAndRefine instances and indexer: merged MTZ byte-identical on three sets; 0.2-2.5 s per run. Also MOSAICITY_DEG (median, P10, P90 over frames) - the frame-order-smoothed sigma_M the merge computes partiality from, Kabsch's sigma_M as XDS's REFLECTING_RANGE_E.S.D. - in the report. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C	2026-09-25 21:00:51 +02:00
leonarski_fandClaude Opus 5.5	19f399a973	Rugnux: write the standard setting, or the user's; match a reference MTZ on its own axes ... The files were written on the axes the space-group search named, which for P2221/P21212 puts the unique axis wherever the a<b<c indexing put it (a 52.51 87.87 137.72 crystal came out P 2 21 21 where XDS writes 87.87 137.72 52.51 P 21 21 2), and a reference MTZ was matched in the data's frame: on permuted axes its free-R flags landed on unrelated reflections while the log reported a high matched count. - New CrystalSetting (scale_merge): changes of basis between settings of one lattice (cell, group, index operator, basis matrix), the {-1,0,1} det +1 candidates (CellMappingOperators, moved from ModelValidation), MetricViolation (moved from Rugnux), ChooseOutputSetting and SeatGroupByAbsences. - Output setting: after every decision the merge, the integrated reflections (unmerged MTZ), the P1 cross-check, the lattice and the _process.h5 reindex matrix are relabelled into the ITA standard setting - or, in priority order, a reference MTZ's, a fitting model's, the -C axis order, a non-standard -S symbol's. Free-R flags are drawn again on the written axes. Reported as SETTING_OPERATOR / SETTING_SOURCE. - Reference MTZ: the group is kept in its setting; after the merge every cell mapping onto the reference cell (times the twin laws) is scored by the reference CC, the best is re-seated and re-merged, and the free flags are inherited only where CC >= 0.5 over >= 50% of the reference range (REFERENCE_MISMATCH otherwise; --mode scale gates the same way). REFERENCE_OPERATOR / _CC / _MATCHED_FRACTION / _FREE_FLAGS_INHERITED. - -S: a fixed group is put on the axes its absences name before merging (SeatGroupByAbsences), fixing -S 18 on a cell whose pure axis is not c. - --model: a model in another setting is now a claim the null tests; where it fits, the data are written in its setting and the validation is remade on those axes (KeepModelVerdict carries the decisions over). Tests: [setting] (synthetic #18/#17/I222/C222/c-unique P21/C2 beta/I2->C2/P1, -C and -S order, absence seating, permuted reference with flags). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C	2026-09-25 20:16:42 +02:00
leonarski_fandClaude Opus 5.5	3de894989c	Report summary: a Supercell line beside pseudo-symmetry and twinning ... The SUPERCELL_POSSIBLE advice now also sits in the summary at the top of the report, with the doubled cell ready for -C; the rule is shared with the warning. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C	2026-09-25 10:20:28 +02:00
leonarski_fandClaude Opus 5.5	dd18d8c21d	Warn SUPERCELL_POSSIBLE where the half-integer class looks like Bragg reflections ... Advisory only: the class is measured (<I/sigma> >= 0.5) and its rocking part is at least 2% of the lattice's, three standard errors clear. The warning asks the user to process both settings - the run's cell and the reported doubled cell with -C - and compare them in refinement. Of 105 battery rotation sets it names 8: both crystals whose accepted cell is the doubled one, one pseudo-translation whose doubled description is an accepted alternative, and five correct sub-cells with weak ordered half-integer intensity. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C	2026-09-25 09:36:25 +02:00
leonarski_fandClaude Opus 5.5	6c9205a670	Report the strongest index-2 superstructure class and the cell it doubles to ... The report-only supercell probe now reaches the results report: SUPERCELL_CLASS (parity of the primitive indices), its occupancy and Bragg-like (rocking) part against the lattice's own reflections, its <I/sigma>, and SUPERCELL_DOUBLED_CELL, the Niggli-reduced cell to give with -C. No decision is taken on it: correct cells whose half-integer class is diffuse, and cells whose depositor kept the sub-cell, cannot be told from a real doubling by the data alone. On a crystal with a real doubled axis the reported cell matched the deposited one, and processing on it with -C brought R_free against the deposited model from 0.60 to 0.29. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C	2026-09-25 08:57:28 +02:00
leonarski_fandClaude Opus 5.5	9e510816e0	Merge hq-cure-merge into hq-pool3; R_MEAS stays the ordinary statistic, the weighted one is R_MEAS_WEIGHTED ... R_MEAS is what users set beside XDS/AIMLESS, so its meaning does not change; the merge-weighted value from hq-cure-merge is reported beside it (R_MEAS_WEIGHTED, REFRES_R_MEAS_WEIGHTED). The per-hand table keeps the ordinary statistic. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C	2026-09-25 06:05:46 +02:00
leonarski_fandClaude Opus 5.5	5c5eb00904	Merge statistics: R_meas weighted as the merge weights each observation ... The delta-CC1/2 disposition keeps a weak stretch in the merge (downgraded) wherever removing it would not raise CC1/2, and the merge then carries each of its observations at the small 1/sigma^2 its scaled-up counting error gives it. R_meas counted those observations at full weight, so the frames that add next to nothing to the intensities set the number. hq-pool battery: 8xtf kept 115 weak frames (scale 0.1-0.2 of the run's) with the same CC1/2, <I/sigma> and CC_model per shell as rc173 with 84 frames rejected, and R_meas was 1.3-1.5x higher in every shell; 9w3y (33 deg rejected -> 0, every model metric better) and lyso_x10sa_strong read the same way. The disposition itself is not segmentation-dependent: conviction is on the batch grid, not the ledger ranges, and those sets' dispositions changed because the corrected data changed. R_meas now weights each observation by its merge weight v = 1/sigma^2 under the error model (corrected_sigma on the host, ModelSigma on the GPU, with the error model of the last MergeAccum), normalised per reflection to Kish's effective count, so equal sigmas give the ordinary formula (WeightedRmeasTerms). Where the proportional term dominates - strong reflections - frames are weighted alike, as in the merge: 8xtf's lowest shell reads 15.0%, the rc173 run with 84 frames rejected 15.2%. The per-hand table is weighted the same way. R_MEAS_UNWEIGHTED / REFRES_R_MEAS_UNWEIGHTED keep the XDS/AIMLESS convention and are what to set beside XDS; the battery scorer records them. MULTIPLICITY stays a count. Effect (weighted / unweighted): lyso_x06da_ref 0.0454 / 0.0479, 8xtf 0.225 / 0.907, insu_I_x06da_ref REFRES 0.072 / 0.232. GPU and CPU paths agree to the last printed digit on lyso_x06da_ref. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C	2026-09-25 04:52:24 +02:00
leonarski_fandClaude Opus 5.5	5c28f35f85	Rugnux: report the oscillation the run integrated at; test the rotation-scale fit on a simulated sweep ... OSCILLATION_RANGE was read off the caller's experiment, so a run that adopted a goniometer rotation scale still reported the file's oscillation; it is now scaled by the adopted k (the starting angle is the stage's and stays). The post-refinement logs the range of k over the leave-a-fifth-out folds instead of a ratio to k - 1, which is meaningless near k = 1. PostRefine_RotationScale: partials of a 180 deg sweep simulated at a known stage rate are fitted back to it (0.97 and 1.0, to 1e-3). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C	2026-09-24 11:37:38 +02:00
leonarski_fandClaude Opus 5.5	257686c6fd	Merge: Wilson outlier test ... The median outlier test needs three observations, so a reflection measured once or twice (one good observation and one artefact, the usual case after Friedel merging) was never tested, and where there were more, a precise-looking artefact (a hot pixel, thousands of counts) could outweigh mates from weak frames and become the weighted median itself. Every observation of the written merge is now also judged against Wilson statistics beyond 4 A: E^2 = I / (epsilon <I/epsilon>_shell), centric and acentric laws, a bound set by alpha = 0.01 expected false rejections per dataset (ln(2N/alpha); twice that for centrics), the lower confidence limit I - z*sigma (own sigma, z from the same budget) required to exceed it, shells whose <I> is not established at that significance not judged, and the bound widened by the dataset's measured tail scale (peaks over threshold on the well-measured shells; 1 for a Wilson crystal, larger under tNCS/anisotropy). An improbable singleton is rejected; one with company only when most of its reflection's other observations are probable and it disagrees with them. The reflection is the group, or the Friedel pair under -A. Search merges are not tested (epsilon is 1 in P1, and the screw rows are the reflections a wrong epsilon would call improbable). The flags are handed to the device merge as pre-rejections, so CPU and GPU agree. Report: OBSERVATIONS_REJECTED_WILSON= (part of OBSERVATIONS_REJECTED=), and the developer report lists each rejected observation (hkl, d, E^2, image, x, y). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C	2026-09-24 07:26:42 +02:00
leonarski_fandClaude Fable 5.1	38bb511d23	Make a first-pass detector tilt no mounting can have prove itself on the spots ... The first-pass rotation fit refines the spindle-perpendicular detector tilt freely, and on a sweep whose seed spots reach only a few degrees of 2theta the keystone that would determine it is a pixel or two. The fit then commits whatever the centroids' own systematics prefer - measured 2.5 deg on one sweep seeded to 11.7 A - and that tilt mispredicts the detector corners by 20-60 px against a 6 px integration disc, collapsing the run from 2.8 A to 6.35 A and biasing the metric-symmetry arbiter to a = b on the way. On synthetic data the same runaway is reproducible: a 1.5 deg detector error on 6 A reflections walks the free fit to 3.9 deg, on 8 A reflections to 37. Three data-driven discriminators were tried first and refuted on the corpus: a blanket restraint (0.13-0.16 A and up to 28% of ISa lost on the crystals whose tilt is largest and real, and in-house runs pinned at a header tilt known to be wrong), the distance's held-out excitation criterion (the rocking angles move by a tenth of their noise whether the tilt is real or not), and a keystone comparison of the fitted and header tilts with the beam free in both arms (236-set battery: ~30 sets moved, one collapsed from P1 to C2, one lost a screw axis; differences of 0.007-0.6 sigma held the header on right and wrong cases alike). For a tilt of a few tenths of a degree the keystone is a fraction of a pixel and nothing in the spots says whether it is real. What separated the cases was the tilt's size: every set the keystone arm moved carries 0.08-0.46 deg, and a survey of 211 corpus sets leaves the file's tilt by more than 0.56 deg on exactly one - a 2theta arm swung out 12.8 deg that its file records as square, which the free fit recovers and the held arm refuses by 90 sigma. So the hardware prior decides whether to ask, and the spots decide. Below 1 deg of walk from the tilt the pass started at the fit is trusted as before, by construction. Beyond it the winning candidate is refined again from its start with the tilt held there - the beam centre taking the shift the tilt is equivalent to, so the header tilt is never paired with a beam fitted beside a refused tilt - and the two are judged as the rounds of one chain already are, on the spots each indexes inside the wide gate: the walked tilt stands only when it leads by more than the count's own noise. A real tilt of degrees has a keystone of tens of pixels over the seed spots and wins outright; an artefact has none and loses on a tie. Held rather than bounded, because a box the fit lands on is the same wrong answer at a smaller size. Decided at the fit, so every pass and arm of a run handles itself and nothing is carried between passes; the unconstrained alternative is re-solved beside a refused tilt too. The chain that drives a candidate to its fixed point becomes a lambda so it can be run on the held candidate. The run logs the walk, what it would have moved the far corner by, the shift the beam took instead and both spot counts; where it was refused the report's REFINED_DETECTOR_TILT is the starting tilt and REFUSED_DETECTOR_TILT what the fit had walked to. Tests: a half-degree tilt is found, kept and not reported as a walk; a walk past the prior is made on synthetic data, and the result's verdict, counts and geometry agree with each other. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_013nW6FNRP1bBJJ8pfHiByAT	2026-09-23 19:01:08 +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	9aae0c2ba7	v1.0.0-rc.169 (#79) ... * Building Jungfraujoch no longer needs zlib or Eigen installed on the machine, and the dependencies the build fetches are pinned and updated to current releases. * rugnux: improvements in indexing, lattice selection and geometry post-refinement, which index crystals that previously returned no lattice and keep the better of the two geometries a run measures. * rugnux: improvements in beam-centre measurement, beam-stop detection and space-group determination. * rugnux: the unit cell reported with a determined space group now obeys that group - a cell whose symmetry was confirmed from the intensities is re-refined under it, and a cell the group cannot describe is reported with a warning rather than as it stands. * rugnux drops the stretches of a rotation sweep whose removal measurably improves the merged intensities and reports what became of every frame, and decides the resolution cut on the crystal's own diffraction rather than on its ice rings. * The rugnux results report is machine-readable - every line that is not `KEY= value` data starts with `#` - and states the build it was written by, its authorship and its terms of use (`REPORT_VERSION= 8`). * `jfjoch_viewer`: improvements in the file manager (CBF frames beside HDF5 datasets, a remembered root), the dataset plots, the inspector and the image statistics, plus a settable font size, a view of the rugnux results report, usable performance over a remote display (`ssh -X`) and a reset of all settings to defaults; the reciprocal-space window is removed. * Broker fixes around DECTRIS collections and dark-mask calibration: re-initialising after a run that never started no longer freezes the broker, a cancelled calibration is abandoned instead of reported as done, and a collection whose start message never arrives ends by itself. Reviewed-on: #79 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-15 17:09:31 +02:00
leonarski_f	77bc0cfe52	v1.0.0-rc.168 (#78) ... * rugnux is substantially faster - a corpus of 145 rotation datasets processes in about two thirds of the time - with identical results. * A crystal whose lattice looks more symmetric than it is because the beam centre is off is no longer processed on the wrong cell. * rugnux prints at startup, and writes at the foot of every results report, a short acknowledgement of the X-ray research community whose methods it implements and of the open-source projects it builds on; `ACKNOWLEDGEMENT.md` now ships in every package beside `LICENSE` and `THIRD_PARTY_NOTICES.md`. Reviewed-on: #78 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-10 13:51:16 +02:00
leonarski_f	a39fd29f77	v1.0.0-rc.167 (#77) ... * `rugnux --model` reports CC(model, data) - the correlation of the merged intensities with the placed, scaled model - by resolution shell, on the same shells as CC1/2, with the reflection count and a significance for each. * `rugnux --model` fits the model's scale, anisotropic B and bulk-solvent parameters on the working reflections only, so the R-free it reports is measured against a model no free reflection helped scale. * The bulk-solvent parameters of `rugnux --model` are searched over their physically meaningful range instead of being fitted without bounds, so a model is never scaled with a solvent term that has silently switched itself off. * The rigid-body placement of `rugnux --model` uses the same bounded bulk solvent as the reported fit, so a model is no longer placed against a target carrying a solvent term with no physical meaning. * `rugnux --model` puts the model into the data's own description of the lattice before placing it, so a model whose cell is written on other axes - I-centred where the run indexed C-centred, a different unique axis, a permuted orthorhombic cell - is placed rather than scored where it was read; `MODEL_CHANGE_OF_BASIS=` and `MODEL_SETTING_AS_READ=` report it when it happens. * The rugnux results report opens with a summary - `VERDICT=` (`OK`, `WARNINGS`, `UNUSABLE`, `FAILED`), `VERDICT_TEXT=`, `PATHOLOGY_FLAGS=` with one closed-vocabulary code per condition that warned, and the `WARNING:` lines, which used to close the file - and the sections after it are renumbered 1-5 with no gaps. * `rugnux --developer` writes the full results report - the pipeline-internal keys and the long explanations the default report now leaves out - and `--finalist-ledger` adds the evidence for every space group the search considered, not only the one it adopted. * The results report warns when the merged data carry no usable signal and when too little of reciprocal space was measured inside the fitted resolution, and omits `FITTED_RESOLUTION` where the CC1/2 curve it is fitted on never falls off. * rugnux detects translational pseudo-symmetry and reports it under the `PSEUDO_TRANSLATION` flag as `TNCS_DETECTED=` and the `TNCS_*` keys - a translation the merged data are exactly invariant under is reported as `UNDECLARED_LATTICE_TRANSLATION=` under `LATTICE_TRANSLATION` instead - and a detected pseudo-translation can no longer buy a false screw axis in the space-group search or hide a twin from the L-test (`L_TEST_VS_TNCS=`). * The space-group search determines glide planes from zonal systematic absences, so a non-Sohncke space group such as P 2_1/c or Pbca is named where the run previously stopped at its Sohncke subgroup; `SOHNCKE_SPACE_GROUP=` carries the best Sohncke group beside it on every run that searched, and a centre of symmetry is never claimed. * Where the cell metric carries more rotational symmetry than the Bravais class the indexer named, the extra rotations are put to the intensities and the space-group search is asked again on the metric's own cell - adopted only where the intensities confirm the higher symmetry - so a lattice that is nearly but not exactly hexagonal, or whose reduction landed in a sub-cell, still reaches its true point group. * Systematic-absence calls rest on the evidence rather than on counts: a screw axis whose absent class the data show extinct is no longer refused because a handful of reflections in it read as present, and `SPACE_GROUP_ALTERNATIVES=` no longer drops a candidate that differs only on a zone the sweep never measured. * A reference correlation measured on too few reflections is refused instead of scored zero, so a run given a reference MTZ is no longer reindexed on an operator that mapped almost everything outside the reference's coverage. * A frame counts as indexed from 6 spots on its lattice rather than 9, so a weakly diffracting crystal whose frames cannot carry 9 is no longer refused the lattice it fits; `--min-indexed-spots` overrides it. * `-C` accepts a known cell in any equivalent description - conventional or primitive, centred or not - instead of only the reduced primitive form, so a centred cell given the way it is published no longer makes the run report that it found no lattice. * Each reflection is corrected for the sensor's quantum efficiency at the angle it meets the detector (attenuation lengths from the NIST tables, which also fixes the spot-width parallax term on CdTe) and for the attenuation of the flight path between the sample and its pixel; `--flight-path air|helium|vacuum` declares the medium - default air, since no file states it - and the report says what was assumed and what it was worth. The unmerged MTZ records the factors in new `QE` and `FLIGHT` columns beside `LP`, so raw counts are `I / LP * QE * FLIGHT`, and `_process.h5` in new optional `qe` and `flight` datasets. * Rotation geometry post-refinement fits the crystal and the detector at once, against the observed spot positions and the observed rocking angles together, so the refined distance depends far less on how wrong the file's distance was. * A coarsely sliced sweep integrates correctly: partials are joined into one rocking event by angle rather than by frame count, so two crossings of the Ewald sphere are no longer summed into one full, and at 0.5 degrees per image or coarser the per-frame geometry refinement accepts a spot whose miss the exposure's own rotation accounts for. * `rugnux --mode scale` reports the detector tilt and direct beam of the geometry it re-scaled at, instead of zeros that read as a flat detector, and no longer warns that no image was indexed on a run whose lattice came from its input file. * Every rotation run that determined a space group and merged reports what the mounting cost: `SPINDLE_LOST_UNIQUE_FRACTION=` is the fraction (0-1) of unique reflections the mounting made unmeasurable under the measured point group, also written to the master as `/entry/MX/spindleLostUniqueFraction` and what the mounting warning fires on; `SPINDLE_SYMMETRY_AXIS_ANGLE_DEG=` / `SPINDLE_SYMMETRY_AXIS_ORDER=` describe the mounting in the `--developer` report. * Stills and grid scans carry a per-image `spindle_blind_fraction` - how much of a rotation sweep's blind cone this orientation would make unrecoverable, 0.5 and above calling for a second orientation - through the CBOR stream, HDF5 (`/entry/MX/spindleBlindFraction`), the plot and scan-result APIs, and the viewer and frontend plots; an absent value means the frame could not be assessed and is not a 0. * The results report's `REPORT_VERSION` is 7. Reviewed-on: #77 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-09 07:25:13 +02:00
leonarski_f	680c36c20d	v1.0.0-rc.166 (#76) ... * `rugnux --mode calibration` writes `<prefix>.json` beside the `.poni`, whose `dataset_settings` member is a `jfjoch_broker` `dataset_settings` body as it stands. * `rugnux` and `jfjoch_viewer` read PILATUS miniCBF sweeps natively, without conversion. * Masters written by other facilities open, including Eiger 1.x and third-party NXmx variants. * `rugnux` measures the beam centre on every run, and indexes with it when the file's value indexes nothing. * A detector swung out on a 2theta arm is placed where the file says it stands, and the calibration can hold the tilt fixed. * `rugnux` writes the unmerged MTZ by default, and a P1 merge beside it, so a wrong space group can be re-merged without reprocessing. * Significant improvements to symmetry handling in `rugnux`: the lattice, the point group, the setting and the systematic absences. * The `rugnux` report gives the resolution the CC1/2 fit reached, beside the range the reflections were written to. * The `rugnux` report gives the twinning statistics measured before the space group was decided, beside the ones measured after. * The `rugnux` report gives the strong-direction diffraction limit, and warns when CC1/2 is not monotone with resolution. * `rugnux` ranks screw axes on the evidence their absences carry, rather than on how many control reflections a candidate happens to have. * Twinning is no longer reported when the L-test contradicts it. * The `rugnux` report gives the detector tilt, the measured tilt and the direct beam beside the beam centre, and a post-refined beam centre is judged against the run's own measurement rather than the file's. * `--no-refine-tilt` holds the detector tilt at the value in the file, instead of zeroing it, when the calibration starts from the spots. * The `jfjoch_viewer` grid scan view draws the cells in the proportion of the scan steps, so the map has the shape of the scanned area. Reviewed-on: #76 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-02 21:17:31 +02:00
leonarski_f	511be0c366	v1.0.0-rc.165 (#75) ... * `rugnux --model` adopts the model's space group as a label where the data were merged in its enantiomorph, instead of reindexing the reflections - which swapped I(+) with I(-). * `rugnux --model` warns, naming the atom, when the anomalous density at the model's atoms comes out inverted, which means the data and the model are in opposite hands. * `rugnux --model` writes an anomalous difference map (`<prefix>_anom.ccp4`) when the merge kept the Bijvoet split, and names the ten model atoms it peaks highest on as `ANOMALOUS_SITE_01`..`_10`. * `MEAN_ATOM_DENSITY_SIGMA` is read from the map by cubic rather than linear interpolation and comes out around a tenth higher; it is no longer comparable with the figure earlier versions printed. * `rugnux --model` reads an mmCIF coordinate file as well as a PDB one, gzipped or not, taking the format from the file's content rather than its name. * A model `rugnux --model` cannot use is reported as a `WARNING:` line in the results report instead of only in the log. * The rugnux results report has a `10. MODEL VALIDATION` section when `--model` was given; `REPORT_VERSION` is 4, `WARNINGS` moves to section 11 and no existing key changed. * The rugnux results report records how the run was invoked, what it cost and what it ran on: `COMMAND_LINE=`, `WALL_TIME=` and `GPU_COUNT=` / `GPU=`. * rugnux says which GPUs it can see before it starts processing. * `rugnux --export-unmerged` also writes `<prefix>_unmerged.mtz` on a `--no-merge` run, and is ignored on a run with no output prefix instead of writing a file called `_unmerged.mtz`. * `/start` asks the writer whether the run can be written before the detector is armed, so a run whose master file already exists, or whose output directory cannot be created, is refused up front with the writer's own message. This needs the TCP image stream or the built-in HDF5 writer; the ZeroMQ stream is unchanged. * A calibration that fails goes to `Error` carrying the reason instead of `Inactive`, so `/wait_till_done` and `/wait_until_running` report it; a cancelled calibration still goes to `Inactive`. * `/wait_till_done` answers 500 with the message when a collection ended in an error. A cancelled collection and a collection that only triggered a warning still answer 200. * A pending start failure is discarded by `/cancel` and `/deactivate`, as it already was by `/start` and `/initialize`. * `/scan_result` no longer reports the previous run's images after a collection that failed to start, or after `/deactivate`. * The TCP image stream protocol version is 4. `jfjoch_writer` and `jfjoch_broker` have to be of the same release, as before. Reviewed-on: #75	2026-08-27 22:16:54 +02:00
leonarski_f	749db470ca	v1.0.0-rc.164 (#74) ... * rugnux now tells you whether a crystal diffracts anisotropically and how far it reaches in each direction, without a second program: a new `9. DIFFRACTION ANISOTROPY` section in `<prefix>_report.txt` and matching `_reflns.pdbx_aniso_B_tensor_*` / `_reflns.jfjoch_aniso_*` items in the merged mmCIF report the anisotropic deltaB, the diffraction limit along each principal direction, and a `NOT DETECTED` / `DETECTED` / `CANNOT DETERMINE` verdict measured against the data set's own systematic error. It is a description only - no intensity is corrected, no reflection is removed, and the merged data do not depend on direction. * rugnux can hand its integrated observations to another scaling program: `--export-unmerged` writes `<prefix>_unmerged.mtz`, an unmerged MTZ readable by aimless, pointless, careless and `iotbx.merging_statistics`, in `--mode mx` and `--mode scale` alike. Each rotation reflection's partials are summed into one full; `--export-unmerged-partials` writes one row per image instead. Intensities carry the Lorentz-polarization factor and nothing else, since those programs scale the data themselves. Lattice-centring absences are not written; screw and glide absences are. * rugnux integrates crystals with broad spots better - where it changes anything, per-shell mean I/sigma improves by up to 31% and R_meas by up to 24% - because on rotation data the integration signal radius is now taken from the crystal's own measured spot width instead of a fixed 4 px. `--adaptive-integration-radius=off` restores the fixed radius and an explicit `--integration-radius` still overrides both. The widened radius applies to the final integration pass only, and a pattern too dense for it is re-integrated at 4 px with a note in the log. * rugnux discards fewer stills reflections for want of a background ring, improving per-shell R_meas over most of the signal-bearing range: the stills background ring now runs to 14 px instead of 12. The gain reverses in shells below a mean I/sigma of about 4. * rugnux determines the space group with thresholds that mean the same thing on a weak crystal as on a strong one: symmetry operators are scored on resolution-normalised intensities (E squared) instead of raw merged intensities, and a reflection counts as genuinely present on its counting significance instead of on the merged I/sigma, which saturates at the merge's own ISa. The search resolution cut is no longer able to move the answer, and the twin-law H bound moves from 1.70 to 1.85, which stops one class of correct high-symmetry assignment being refused as twinning. * rugnux says what the space-group search tested and what it could not: the twin-law disagreement H is printed for every operator together with the adopted point group's H ratio and its bound; alternatives that are not on the reported lattice are named with how their cell differs; and a lattice centring the data could not test - the crystal having been integrated on the primitive sub-cell, so the reflections it extinguishes were never measured - is marked `UNTESTED` and warned about where it is adopted, as coming from the lattice metric rather than from the intensities. * rugnux `--mode scale` re-merges a `_process.h5` in the right symmetry without being told it: the file now records the space group on every run - a two-pass rotation run wrote none before, so re-merging defaulted to P1 - together with the change of basis under `/entry/MX/reindexMatrix` where the lattice was re-seated, and `--mode scale` also reports the Wilson B-factor estimate instead of `WILSON_B= nan`. A file written before this stops with a message naming the two cells and the override to use, instead of failing inside the merge. A third-party reader of a `_process.h5` must apply `reindexMatrix` where it is present. * rugnux installs on its own, as a package called `rugnux` - `dnf install rugnux` or `apt install rugnux` - instead of arriving inside `jfjoch-viewer`. It pulls in none of the acquisition stack, so a machine that only processes data no longer has to carry the broker, the detector libraries or Qt to get it. Installing it over a `jfjoch-viewer` from rc.163 or earlier, which still owns `/usr/bin/rugnux`, upgrades cleanly rather than failing on the duplicate file. * rugnux is also a standalone download, built for arm64 as well as x86_64: `rugnux-<version>-linux-{x86_64|aarch64}-cuda<major>.tgz` and `rugnux-<version>-win64-cuda<major>.zip` on the release page, for machines that are not managed by a package manager. The aarch64 build targets GH200 and DGX Spark, and is untested on hardware. * Every portable Linux binary is now a single self-contained file: cuFFT is linked statically instead of being shipped beside the executable and found through an rpath, so `rugnux` and `jfjoch_viewer` need nothing but an NVIDIA driver, and only to use the GPU. The `.rpm`/`.deb` continue to take cuFFT from the distribution. The developer utilities `jfjoch_extract_hkl` and `jfjoch_recompress` are no longer packaged anywhere. * Jungfraujoch needs six fewer shared libraries on the machine - libopenblas and libmetis, and libgfortran, libquadmath, libgomp and libz behind them - because the Ceres LAPACK, METIS and SuiteSparse back-ends are no longer built. Nothing in the code ever selected them, and results are unchanged. * The PCIe driver DKMS package builds for the kernel it is being installed for instead of the running one, so a module built while a kernel update is being applied loads after the reboot. * The PCIe driver builds on RHEL 9.5 and later, and on their CentOS Stream, Rocky and AlmaLinux equivalents, where the `vm_flags` kernel interface was backported into the 5.14 kernel. * A data collection started with `async_start` that fails to start - a writer refusing to overwrite an existing file, for instance - is reported as an error by `/wait_until_running` and `/wait_till_done` instead of as a timeout and a successful collection respectively. The error message is the one the writer gave. * A calibration that is cancelled or that fails to collect its pedestals is no longer reported as a successful one. The broker goes to `Inactive` with an error message and has to be initialized again, instead of sitting in `Idle` looking ready to measure while holding partial pedestals - data collected in that state was silently mis-converted. * A failed `/initialize` is reported to `/wait_until_running` and `/wait_till_done` as soon as it happens, instead of when their timeout expires. * `space_group_number` accepts space groups up to 230 in the API schema, so cubic space groups can be recorded. The broker always accepted them; the generated clients rejected them before the request was sent. * The results report's `REPORT_VERSION` is 3, two sections having been added. Existing key names and table columns are unchanged. * The merged statistics table has **9** resolution shells instead of 10, which is what XDS reports. The bins were already XDS's - equal steps in 1/d^2 between the lowest- and the highest-resolution reflection the merge kept - so at the same resolution limits the two tables now have the same shell boundaries and can be read row for row. `--resolution-shells` sets a different count. * `rugnux --model` now settles the frame the merged reflections are written in, not only the frame the R-factors and the maps are computed in: the `.mtz`/`.cif`/`.hkl` come out in the model's indexing, and where the data were merged in the model's enantiomorph they take the model's hand and space group - which on anomalous data puts I(+) and I(-) the right way round. The indexing choice is logged with the winning R-free and the runner-up, so a decision made within noise is visible. * `rugnux --model` can resolve the indexing ambiguity of a **serial stills** run, which a model could not do before: structure factors computed from the model become the per-image reference, the same role a reference MTZ plays. It needs the cell and space group up front (`-C` / `-S`). Without one or the other, a merohedral serial run still merges both hands together and says so. * The rugnux documentation opens with a quick start - the default run, and runs with a reference MTZ, with a model, or with the space group and cell pinned - and explains the indexing ambiguity: what it costs on rotation and on serial data, and which of `-z` / `--model` resolves it in each case. The long reference pages now carry a table of contents. Reviewed-on: #74 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-08-26 22:47:00 +02:00
leonarski_fandjungfrau	4dc2534dbf	v1.0.0.rc-162 (#72) ... **Files written by Jungfraujoch now import correctly in DIALS, XDS and pyFAI.** A tilted detector, a grid scan, a still recorded at a goniometer position, and saturated or unreadable pixels were each described in a way that a third-party program acted on wrongly. If you process Jungfraujoch data outside Jungfraujoch, prefer this release to any earlier one. * HDF5: the detector tilt (`rot1`/`rot2`/`rot3`) is exported correctly in the NXmx transformation chain; untilted geometries are unaffected. * HDF5: a still recorded at a goniometer position is no longer read back as a single image, and a grid scan records a stationary spindle so a program that requires a rotation axis can open it. * HDF5: the sample transformation chain is written in mounting order, with a Smargon head position told apart from the spindle, one entry per image, `module_offset` as a float unit vector, and `offset_units` on every offset. * HDF5: saturated, underloaded and unreadable pixels are described so a downstream program masks them - `saturation_value`, `underload_value`, `error_value` and `bit_depth_readout` are written correctly, and a data file missing next to a VDS master reads as the error marker rather than as zero counts. * HDF5: the rotation axis is read back under whatever name it carries, and `mirror_y` records whether the assembled image is mirrored in Y relative to the detector's raw readout. * A grid scan and a goniometer axis can both be set; they are no longer alternatives. * `images_per_file` is chosen from the acquisition when it is not given: a rotation sweep of at most 20000 images goes into a single data file, a grid scan splits on whole fast-axis rows, and stills and serial keep 1000. * The writer refuses a stream whose start message declares a different pixel format than its images carry, and a DECTRIS detector sending signed images is no longer declared unsigned. * The image stream can carry the sample transformation chain (`transformations`, in the END message); a producer that does not send it gets the same chain built by the writer. * rugnux: fixing the space group with `-S` no longer prevents the lattice from being found - a lattice indexed in a different setting is reindexed into that group's own setting, and a run whose crystal does not have that group's lattice stops and names the cell it indexed as, rather than reporting statistics that cannot describe it. * rugnux: the per-image resolution estimate now predicts the resolution the merged data reach rather than the highest-resolution spot found, and is reported as `SPOT_RESOLUTION_ESTIMATE`. * rugnux: two runs of the same command on the same images produce the same merged intensities; the azimuthal profile written alongside them is not yet reproducible in the same way. * rugnux: the offline lattice refinement is bounded by iterations rather than by a wall clock, so a loaded machine can no longer refine to a different lattice; a live acquisition keeps its real-time bound. * rugnux: the detector-frame modulation correction is fitted on a grid spanning the detector, so whether it is applied no longer depends on how far integration reached. * rugnux: the geometry pre-pass no longer writes `<prefix>_01.mtz`, `_01.cif`, `_01.hkl` and `_01_image.dat`; the refined second pass writes those files under `<prefix>`, and that is the result to use. * rugnux: `_process.h5` describes the pixel format of the images it links to, and is written on a thread of its own. * rugnux: the detector geometry is also logged in XDS's convention (`ORGX`/`ORGY`, detector axis vectors, rotation axis), so it can be compared with an XDS refinement. * rugnux: an image integrated in pyFAI through the `.poni` file written by `--mode calibration` comes out with the correct azimuth, and the file declares pyFAI's `orientation`, which needs pyFAI 2024.01 or newer. Radial integration is unchanged. * rugnux: a rotation run is substantially faster throughout - beam-stop detection, first-pass indexing, geometry refinement, integration, scaling and merging - and observations outside the scaling resolution range are dropped as they are ingested. The refined geometry, the space group chosen and the merged statistics are unchanged. * Faster spot finding and indexing, on the broker as well as in rugnux; the spots found and the lattices indexed are unchanged. * A run reserves substantially less GPU memory: nothing is allocated for buffers that are never read, and a worker builds only the engines it uses. * rugnux: with `-N` left at its default the per-image loop of `--mode mx` uses at most 16 workers per GPU, rather than one per hardware thread; an explicit `-N` is obeyed as given. * CUDA 12 builds now contain device code for Volta, so the RHEL 8 packages and the portable Linux `.tgz` run on a V100; the CUDA 13 artefacts (RHEL 9, Ubuntu, Windows) remain Turing and newer. * The build resolves a single Eigen for the whole project, and refuses to configure if Ceres picks up a different one; a build that mixed two Eigen versions was undefined behaviour and crashed at -O2. * Documentation: a security page, and the supported GPU generations and minimum NVIDIA driver version of every released artefact. **Breaking change to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.162, `frontend/src/client`): * `dataset_settings.images_per_file` is no longer `default: 1000` and no longer accepts `0`; it is optional, and its minimum is 1. A client sending `0` (previously "one file for the whole run") is now rejected - omit the field instead, which for a rotation sweep gives the same single file. * `file_writer_format` now defaults to `NXmxVDS`, matching the server's own default and the layout recommended for DIALS, XDS and CrystFEL. A generated client that fills in schema defaults and does not set the format explicitly will write VDS masters where it previously wrote legacy ones; set `NXmxLegacy` explicitly to keep them. --------- Co-authored-by: jungfrau <jungfrau@mx-aare-test.psi.ch> Reviewed-on: #72 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-08-25 08:21:39 +02:00
leonarski_f	538f3504d3	v1.0.0.rc-161 (#71) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * **rugnux: significantly better quality of results, and faster.** A large rework of integration, scaling, merging, geometry refinement and space-group determination, together with measurements the program previously made no attempt at - the direct beam before indexing, the beam stop, the goniometer rotation scale, and the stretches of a sweep the crystal did not deliver. A rotation dataset typically gains observations at better <I/sigma> and R_meas, and every `mx` and `scale` run writes a `<prefix>_report.txt` results report modelled on XDS's `CORRECT.LP`. Many defaults moved with it: spot detection is self-calibrating, beam-stop detection and rotation geometry post-refinement are on, resolution limits default to as far as the detector reaches, and ice-ring handling engages only where the crystal is measured to have ice. * **jfjoch_viewer:** the beam-stop shadow, the detector calibration and the beam-centre measurement are reachable from "Analyze dataset"; the settings panel reports how the sample moved and how polarized the beam was; image rendering and interaction are faster. * **Performance:** bitshuffle+LZ4 images are decoded on the GPU rather than on the host, with the bitshuffle inverse fused into preprocessing so the decompressed frame is never held in device memory. * **Broker, writer, packaging and build:** image-slot lifetime and locking fixes, per-image datasets sized by the images actually written, the Debian/Ubuntu broker package renamed to `jfjoch`, and `image_analysis` compiling under MSVC again. **Breaking change to the rugnux command line:** * `--azint-only` and `--scale` are **removed**, replaced by `--mode azint` and `--mode scale`; the full pipeline is `--mode mx` and remains the default. A script passing the old flags now fails with the list of valid modes rather than silently running the wrong one. * `-t`/`--stride` is **refused on rotation data**: skipping frames cuts every reflection's rocking curve, so the combined fulls and their partiality would be measured over frames the sweep never recorded. Select a contiguous range with `-s`/`-e` instead. `--mode azint` and `--force-still` still take a stride. **Breaking changes to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.161, `frontend/src/client`) or read the affected fields as optional: * `image_scale_b` is removed from the `plot_type` enum, so a client requesting that plot now gets an error rather than a curve. * `azim_int_settings.high_q_recipA`, `spot_finding_settings.high_resolution_limit` and `spot_finding_settings.low_resolution_limit` are no longer `required`. All three mean "no limit at that end" when unset and are omitted from the response instead of carrying a placeholder value, which raises in a client generated from an rc.160-or-earlier spec. A value of 0 is still accepted and means the same thing. **Breaking changes to the stored formats** - a consumer reading these fields must treat them as optional: * The per-image image-scale B factor is no longer computed, so `/entry/MX/imageScaleBFactor` is absent from newly written HDF5 files and the corresponding key is absent from the CBOR DataMessage and END blocks. Files written by rc.160 and earlier still contain it and still open; nothing in the pipeline reads it any more. * `_reflns.jfjoch_diffrn_ISa` now carries the whole-range `1/sqrt(a*b)` that XDS's ISa denotes, and the error-model `a` and `b` are reported in XDS's convention; the strong-reflection asymptote moves to `_reflns.jfjoch_diffrn_ISa_asymptotic`. **A file written by an earlier version carries the asymptote under the plain `ISa` name.** Reviewed-on: #71 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-08-13 17:03:10 +02:00