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Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	547d2f5fa6	Pre-flight: check the master file, not every data file of the run ... 5f838bdb2 widened CheckOutputFilesAvailable from the master file to every data file the run will write, so a stale _data_000001.h5 would be caught up front rather than at the rename. The enumeration is unbounded: it is one std::filesystem::exists per planned file, so a long run with a small images_per_file - it can be set to 1 - is thousands of lookups, and they run inside the 5 s PREFLIGHT ACK budget that BUSY heartbeats do not extend. On a shared filesystem that turns a writable output into an "ACK timeout", which is both wrong and unreadable. It also called HDF5Metadata::DataFileName for every planned file, and that throws past file 999999 (9999 on SwissFEL), refusing a run up front on a file number the acquisition would never reach. Back to the master file alone, which is what the constructor checked before. A data file in the way is caught per-writer at finalize again, as it was. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016L1qig74oYQzfUJJZbbxFh	2026-08-27 16:04:52 +02:00
leonarski_fandClaude Opus 5	6dd36436b6	rugnux: the unmerged MTZ is written on request again, not on every run ... 0fed51f76 made <prefix>_unmerged.mtz default-on so a run that turned out to need it would not have to be repeated. It costs more than that is worth: measured on a dense rotation dataset, it adds 2.6 s to a 7.0 s --mode scale run (+38%) and writes 272 MB - larger than the merged .mtz, .cif and .hkl put together, and paid by every run whether or not anything will read it. --export-unmerged asks for it again. --no-export-unmerged stays accepted and now does nothing, the mirror of what --export-unmerged did while the default was on. The two fixes that came with the default-on change are kept: the file is written in --mode mx and --mode scale and with --no-merge, and both write sites are guarded on the output prefix, so a prefix-less run no longer writes a file called "_unmerged.mtz". Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016L1qig74oYQzfUJJZbbxFh	2026-08-27 16:04:52 +02:00
leonarski_fandClaude Opus 5	ab14ca10e8	Reindex into the ASU: follow the change of hand, not the hand landed on ... ReindexMergedIntoAsu swapped I(+)/I(-) whenever the reindexed index came out on the minus side of its Friedel pair. That is right only for a row that started on the plus side, which is every row when merge_friedel is set - and none of the problem cases. With the mates kept apart, the merge stores the plus mate at +hkl_asu and the minus mate at -hkl_asu (Merge.cpp), while RotationScaleMerge attaches I_plus / I_minus in the plus convention on both rows alike, keying the lookup at plus=true. An alternative-indexing operator is rotation-type, so op(-x) == -op(x) and the two mates always land on opposite sides: testing key.plus alone therefore swaps exactly one row of every pair, whichever way the operator went. The pair ends up self-contradictory, and the mmCIF's pdbx_I_plus / pdbx_I_minus and the F(+)/F(-) columns are swapped on half the rows. Reached by "rugnux -A --model model.pdb" - -A clears MergeFriedel - on a crystal whose indexing ambiguity the model resolves, which is the one path that both keeps the mates apart and reindexes. The swap now fires on was_plus != key.plus. With merge_friedel every row is stored at the ASU representative, so was_plus is always true and this reduces to the previous test; the existing change-of-hand case is unchanged. The test that covered the merge_friedel=false path checked only I, so it passed either way. The new one builds both mates of a pair and asserts they still agree about which intensity is which afterwards - an invariant that holds however the operator moves the hand, so it fails on the old code for either direction. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016L1qig74oYQzfUJJZbbxFh	2026-08-27 16:04:37 +02:00
leonarski_fandClaude Opus 5	dee539a713	rugnux: --model takes the model's enantiomorph as a label, and stops flipping I(+)/I(-) ... Where the data were merged in the enantiomorph of the model's space group, --model reindexed the observed reflections by change_of_hand_op(). That was wrong, and the anomalous site list added yesterday is what showed it. The two groups of an enantiomorphic pair differ only in the translations of their operations. Their rotations are identical, so they transform hkl identically, share a reciprocal ASU, and split into Bijvoet hands identically - to_asu_sign returns the same answer for either, verified over 200k random indices for all eight enantiomorphic families. The label therefore carries no handedness at all, and there was never anything about it to undo. What does carry the hand is the indexing the data already have, from the diffraction geometry, and with it the sign of every anomalous difference. change_of_hand_op is the inversion, so reindexing by it swapped I(+) with I(-): it did not correct the hand, it flipped it, on the strength of a label the space-group search itself reports as undetermined. So the model's group is now adopted as a label and no reflection moves. On a tetragonal reference dataset the site list goes from ten unrelated atoms at around 3 sigma to the two ordered halides at 15.6 and 10.3 sigma followed by the methionine and every cysteine sulfur at 6.6 to 7.3 - the correct map was there all along and the reindex was inverting it. Whether the model and the data agree about the hand is a real question, and now an answerable one: a map whose deepest hole at an atom is below -5 sigma and deeper than its highest peak says they disagree, and the run warns and names that atom. It is deliberately not repaired by reindexing, which would make the two agree by construction and destroy the evidence for which of them is wrong. Verified by mirroring a model: the warning fires naming the atom at -10.1 sigma, where the unmirrored model reads +10.1. R-free is identical to four decimals across that mirror, which is exactly why it could never have arbitrated this. MODEL_HAND_OPERATOR becomes MODEL_ENANTIOMORPH_ADOPTED, there being no operator to report. REPORT_VERSION stays 4: both that version and the MODEL VALIDATION section it describes were added in this same unreleased cycle, so no report carrying the old key has ever left it and there is nothing for a consumer to have depended on. The unmerged export follows only the indexing operator now, the enantiomorph being a label. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_014zTy4Bpi4pPHw4bybf7q2R	2026-08-27 15:09:24 +02:00
leonarski_fandClaude Opus 5	6e2873514f	rugnux: read the 2Fo-Fc map at the atom centres cubically too ... Grid::interpolate_value defaults to trilinear, and on the d_min/3 map grid that under-reads a peak by around a tenth. The anomalous site list already asks for cubic; MEAN_ATOM_DENSITY_SIGMA was left on the default so a number already in existing reports would not move, but the same argument that makes cubic right for one reading makes it right for the other, and the two should not disagree about how a map is sampled. One named constant now carries the choice and the reason for both. Measured on two rotation datasets: 1.96 -> 2.20 and 2.69 -> 2.89 sigma. The maps, the R-factors and every other reported number are unchanged - only this reading of the map moves, so it no longer compares with what earlier versions printed. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_014zTy4Bpi4pPHw4bybf7q2R	2026-08-27 14:56:04 +02:00
leonarski_fandClaude Opus 5	b0234a1b4b	rugnux: --model names the strongest anomalous scatterers, not just R-free ... Where the merge kept the Bijvoet split - which the default Friedel-averaged merge does, so this needs no -A - --model now computes an anomalous difference Fourier, coefficients F(+)-F(-) on the model phase turned back by 90 degrees over the acentric reflections, writes it as <prefix>_anom.ccp4, and reads it at the model's own atom centres. The ten highest are logged and land in the results report as ANOMALOUS_SITE_01..10, each named by the atom, residue and chain it sits on, with its height in map sigma. Reading at the sites rather than searching the map for blobs is what ANODE does, and it says what carries the signal instead of leaving coordinates to look up; a scatterer the model does not contain is by construction absent from the list, which is what the map file is for. The list is always ten long, so its information is in the heights. On an S-SAD dataset at 5 keV the six cysteine sulfurs take ranks 1-6 (10.1 down to 4.2 sigma) and rank 7 falls to 2.2; the same crystal at 13 keV, where sulfur has no anomalous signal to speak of, tops out at 2.7 sigma with a water and a main chain carbon inside the top five. So the same list reads as a signal / no-signal gate, not only as a ranking. The reading is cubic. Grid::interpolate_value defaults to trilinear, and on the d_min/3 map grid that under-reads a peak this sharp by up to a quarter, unevenly enough to reorder the sites; cubic on the same grid is within about 2% of a sample-rate-10 one. The map r.m.s. is unchanged by the sample rate, so the normalisation was never at fault. The 2Fo-Fc reading behind MEAN_ATOM_DENSITY_SIGMA is deliberately left on the default so a number already in existing reports does not move. An anomalous merge keeps each Bijvoet mate as a row of its own and both rows carry the same F(+)/F(-) pair, attached to the + index of the Friedel ASU of the frame the merge was made in, so the differences are read from the merged reflections as they came in - carried into the model's frame here, on the + rows only. Taking the - rows as well would give one reflection both signs of its difference and let the last row written decide. write_ccp4 splits into an FFT and a write so the anomalous map can be both written and sampled from one transform; the 2Fo-Fc atom-centre score, which used to repeat that FFT, now reuses the grid. Cross-checked against ANODE run on this output: identical identification - its three peaks are the three disulfides, each maximum 0.64-0.70 A off a sulfur we name - with our heights about 1.35x lower. Sharpening, grid and sigma normalisation are excluded; the residual is SHELXC's FA preparation, which fed ANODE 2166 reflections against our 2534. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_014zTy4Bpi4pPHw4bybf7q2R	2026-08-27 14:51:06 +02:00
leonarski_fandClaude Opus 5	bc500d1578	rugnux: report what --model found, and attribute GEMMI's bundled headers ... Two things left open by the previous commit. A model that was validated left nothing in the results report. R-work, R-free, the bulk-solvent parameters and the map filenames went to the log and nowhere else, so a run given --model was, in the file anyone reads afterwards, indistinguishable from one that was not - and the WARNING line added last commit was the only trace of a model that failed. Section 10. MODEL VALIDATION now carries it: MODEL_FILE, the space group the model is in, R_WORK / R_FREE with their reflection counts, the bulk-solvent k_sol / b_sol and overall scale, the mean 2Fo-Fc density at the atom centres, the hand and indexing operators the written reflections were brought into the model's frame with, and MAPS_PREFIX. A model that could not be used gets MODEL_VALIDATION= NOT_PERFORMED and the reason instead, in the shape the merging section already uses. A run that asked for no model has no section at all. That moves WARNINGS from 10 to 11, which is what REPORT_VERSION is for: it is now 4. No existing key was renamed and no table column moved, so a consumer that greps for what it needs is unaffected; one that keys on the section number of WARNINGS is not, hence the bump. The four third-party headers GEMMI has always bundled - fast_float, half, pocketfft and tinydir - were never listed in THIRD_PARTY_NOTICES.md, riding instead under GEMMI's single MPL-2.0 row. They are other authors' code under other licences (Apache-2.0 OR MIT OR BSL-1.0, MIT, BSD-3-Clause, BSD-2-Clause), and MPL-2.0 does not speak for them. Each now has its own row and its own licence text, alongside the PEGTL and sajson entries added with the CIF parser, and a note records why the six are listed separately from GEMMI. Their terms live in the headers rather than in LICENSE files, so five of the six texts are kept by hand; COLLECT.sh says so and copies the one - PEGTL - that ships a file. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016WmryXe8ASbNi632sUMfsa	2026-08-27 13:50:13 +02:00
leonarski_fandClaude Opus 5	2e8040c60c	rugnux: read mmCIF models with --model, and say when a model could not be used ... --model called gemmi::read_pdb unconditionally, so a coordinate file in mmCIF - which is how the PDB serves coordinates by default - was refused outright: Model validation: cannot read model 6G8A.cif: Incorrect file format (perhaps it is cif not pdb?) Worse than the refusal was what followed it. ValidateAgainstModel logged, returned an empty result, and the run went on to finish with exit code 0, no R-free, no maps and nothing in the report - indistinguishable from a run that was never given --model at all. A script that passed a .cif, checked the exit code and grepped for R-free simply got nothing back. Both read sites now go through read_structure_gz with CoorFormat::Detect, so PDB, mmCIF and mmJSON are all read, gzipped or not, and the format comes from the file's content rather than from its name. Detect is passed explicitly: GEMMI otherwise takes the extension and only falls back to the content when it does not recognise one, and a model arrives named however whoever produced it named it. That needed a part of GEMMI the vendored subset had trimmed away. mmread.hpp was already here but its CIF parser was not, so this restores what upstream GEMMI ships: read_cif/mmcif/json/mmread_gz, plus GEMMI's own copies of PEGTL (MIT, Colin Hirsch and Daniel Frey; 155 headers, 672 kB) and sajson (MIT, Chad Austin; one header). Both are listed in THIRD_PARTY_NOTICES.md with their own licence texts, PEGTL's collected by COLLECT.sh and sajson's kept by hand, its terms being a comment block rather than a file. json.cpp carries a one-line change: upstream keeps sajson at the root of its repository, outside the include tree this subset copies, so the include points at where the other bundled headers live. ModelValidationResult gains failure_reason, and a model that was asked for and could not be used now reaches the results report as WARNING: Model validation did not run: model bogus.pdb has no atoms or no unit cell in --mode mx and --mode scale alike. The run still succeeds - a merge that is good is not made bad by a model that was not - but it no longer does so quietly. One log line was making a claim it could not support: the indexing-ambiguity message said the ambiguity was "resolved against the supplied model" while being printed before the model is read, so it announced a resolution that a failed model never performed. It now says the model will be used; the reference branch, where the work really has already happened, keeps the past tense. Verified on the rotation test dataset with a deposited mmCIF, the same file gzipped, an mmCIF under a .pdb name, a PDB, and an unreadable file. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016WmryXe8ASbNi632sUMfsa	2026-08-27 13:42:48 +02:00
leonarski_fandClaude Opus 5	e65cfdc675	rugnux: record in the report how the run was invoked, what it cost and what it ran on ... The results report said what the run determined but nothing about how it was produced, so a report read next to a lost shell history could not be reproduced or compared. Four keys in the header block, all new, none renamed - a consumer that greps for what it needs is unaffected, so REPORT_VERSION does not move: COMMAND_LINE= rugnux -o myrun --model model.pdb dataset_master.h5 WALL_TIME= 262.41 GPU_COUNT= 4 GPU= 4x NVIDIA A100-SXM4-80GB The command line is argv as one shell-ready line; an argument that would not survive being pasted back into a shell is single-quoted, so a file prefix with a space comes back as the one argument it was. It replaces the raw argv echo at the top of the run, which had no quoting at all. WALL_TIME is the whole invocation, timed from the top of the CLI. It is deliberately not result.total_time_s, which starts inside Rugnux::Run and so counts neither opening the file nor setting up the analysis - and which --mode scale never sets at all, having no ProcessResult of its own. It is printed on stdout as well, next to the processing time it is slightly larger than. The GPUs are the reason rugnux is fast, and until now nothing said whether any were being used. get_gpu_names() reports them per device and get_gpu_description() collapses repeats, so four identical cards read as one line rather than the same name four times and a mixed machine keeps one group per model. Both have a CPU-only implementation, so the JFJOCH_USE_CUDA=OFF build reports GPU_COUNT= 0 rather than failing to link. The same line is printed at startup, before the run rather than after it: a machine that turns out to have no GPU - a driver mismatch, a CUDA_VISIBLE_DEVICES left over from another job - is worth knowing about while there is still time to stop, not once the run has taken an order of magnitude longer than it should. GPU_COUNT= 0 is written with no GPU= line beside it, because the absence is the statement. The header comment claiming timing is deliberately absent from the report is now wrong and says so: rates and per-image costs stay on stdout, the total does not. Verified on the rotation test dataset in both build configurations, with and without CUDA_VISIBLE_DEVICES, in --mode mx and --mode scale. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016WmryXe8ASbNi632sUMfsa	2026-08-27 13:09:54 +02:00
leonarski_fandClaude Opus 5	047d58d111	Version 1.0.0-rc.165 ... Generated clients, Redoc, frontend, docs, FPGA and PCIe driver version strings regenerated by update_version.sh. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016WmryXe8ASbNi632sUMfsa	2026-08-27 12:26:35 +02:00
leonarski_fandClaude Opus 5	0fed51f767	rugnux: write the unmerged MTZ on every run, not on request ... <prefix>_unmerged.mtz is what another scaling program needs - aimless, pointless, careless, iotbx.merging_statistics - and a run that did not ask for it up front had to be repeated to get it. It is now written on every run that has an output prefix, in --mode mx and --mode scale and with --no-merge, alongside the merged files and replacing none of them. --no-export-unmerged turns it off; --export-unmerged is still accepted and now does nothing. The summed form is the default one, as before: each rocking event's partials combined into one full, written at the batch its rocking curve is centred on. --export-unmerged-partials still additionally writes the unsummed <prefix>_unmerged_partials.mtz for a program that would rather sum them itself. Both write sites gated on the export flag alone and would have written a file called "_unmerged.mtz" when there was no output prefix. That could not happen while the export was opt-in and a prefix was implied by asking for it; with the export on by default it would fire on any prefix-less run. They now use the same guard the merged writes use. Verified on the rotation test dataset: written by default, by --mode scale and under --no-merge, absent with --no-export-unmerged. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016WmryXe8ASbNi632sUMfsa	2026-08-27 12:24:54 +02:00
leonarski_fandClaude Opus 5	5f838bdb26	Broker: refuse a run the writer cannot write before arming the detector ... A writer refusing to overwrite an existing file was reported badly, and the earlier fix only covered half of it. The commit message of a6a715703 states the assumption that broke: "SendStartMessage precedes every std::async in the receiver constructor". That is true of JFJochReceiverFPGA, where the start message goes out from the constructor body, and false of JFJochReceiverLite, where it goes out from MeasurementThread - launched by std::async from the constructor, which waits only on data_analysis_started. On the DECTRIS path the writer's refusal therefore cannot reach services.Start(); it arrives from services.Stop(), i.e. the second try-block of the state machine's MeasurementThread, which never touched start_exception. /wait_till_done answered 200 for a run that never wrote anything. Two changes, in front of the problem and behind it. In front: a PREFLIGHT frame (TCP protocol version 3 -> 4), sent to every writer before the receiver is built and before the detector is armed. It carries the same CBOR start message a START does and asks one question: could this run be written? The writer runs FileWriter::Preflight - the first three statements of the FileWriter constructor, stopping short of the only one that creates anything - and answers with an ACK. Shared code, so a pre-flight that passes cannot be contradicted by the start behind it. A refusal is not fatal: nothing was started, the connection stays usable, and above all no series is left armed waiting for a trigger that will not come. Both ends already reject a frame of another protocol version, so the bump costs no compatibility. The check now covers the data files, not only the master. A stale _data_000001.h5 used to sail through and fail when the file was renamed into place at the end of the run, after the whole dataset had been collected. The writer holding the master file checks for all of them - they share a directory by construction, the master linking them by relative name - so the siblings do not race each other statting files the others are creating. Behind: /wait_till_done maps an Idle state to 200 or 500 by the severity of the end-of-run message, so a collection that lost packets, or whose writer could not write, is no longer indistinguishable from a good one to a script. A cancelled collection is not affected - MeasurementThread checks the cancel before it looks at the completeness of the data, and reports it with Info severity - and a warning is still a 200. start_exception is untouched. The PREFLIGHT payload is built from FillMessage alone, which is what keeps it small: the per-pixel arrays are added by SendStartMessage and are not in it. Measured on a JUNGFRAU 9M, 1.4 kB against 543 kB for the start message. It is deliberately the whole of FillMessage rather than the fields the check reads today - a hand-picked subset would answer for a different set of file names the day the check learns to read one more field, and would do it silently. Three defects found on the way: TCPImagePuller republished a PREFLIGHT as a real start message, announcing to downstream consumers a run that was not going to happen. TCPStreamPusher::run_number was a plain uint64_t written by the control thread and read by every ACK thread; Preflight adds a second writer to it. StreamWriter::CollectImages reprocessed the last frame whenever WaitForImage returned false - run is only tested at the top of the loop - so an abort wrote the last image a second time. Pre-existing; the new branch made it visible. Verified against a running broker on the local configuration: a colliding master file and a colliding data file are both refused by /start, /wait_until_running and /wait_till_done with the writer's own message, and the log shows the receiver was never started for either; a cancelled collection still answers 200. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016WmryXe8ASbNi632sUMfsa	2026-08-27 12:20:29 +02:00
leonarski_fandClaude Opus 5	5dafb9d21c	Docs: stop the rugnux examples implying that parallelism has to be asked for ... Every example command carried -N 32, which reads as though a run is single-threaded until told otherwise. It is not: the thread count follows the machine, and -N is there to limit it, or to lift the per-image loop's default ceiling of 16 workers per GPU. The examples drop the flag and the quick start says what -N is actually for. Two things the quick start left to be discovered elsewhere: -S takes a Hermann-Mauguin symbol or a space-group number, either spelling; and --model, where the model is isomorphous, pins the enantiomorph - which no measurement can decide - so the merged reflections come out in the model's hand and its space group, and on anomalous data that is what puts I(+) and I(-) the right way round. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Vi1gV6Z45aZL5wLwe85Ksn	2026-08-26 21:31:13 +02:00
leonarski_fandClaude Opus 5	daac3c2da1	rugnux: report nine resolution shells, as XDS does ... The binning rule was already XDS's: equal steps in 1/d^2 between the lowest- and the highest-resolution reflection the merge kept, anchored on the data rather than on the nominal low-resolution cut. Only the count differed - ten shells against XDS's nine - so at the same resolution limits neither the boundaries nor the reflection populations matched, and a per-shell number could not be read across. Forced to nine on a tetragonal rotation dataset, rugnux now gives 4.27 3.03 2.47 2.14 1.92 1.75 1.62 1.52 1.43 against CORRECT.LP's 4.26 3.02 2.47 2.14 1.92 1.75 1.62 1.52 1.43; the hundredth of an angstrom in the first two shells is each program anchoring on its own lowest-resolution reflection, the two sets of survivors not being identical. This matters most to the comparisons that are made shell by shell. rugnux_vs_xds.py hands XDS's resolution range to rugnux but not its shell count, so its low-resolution R_meas column compared a shell running to 4.49 A against one running to 4.26 A - 814 unique reflections against 943. The outer shell was nearly immune, its inner edge being d_min*sqrt(n/(n-1)), which is 1.51 at ten shells and 1.52 at nine. --resolution-shells still sets any count. rugnux_stills_ab.py pins the count for both its arms and now pins nine, so its tables read the same way as everything else. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Vi1gV6Z45aZL5wLwe85Ksn	2026-08-26 20:24:34 +02:00
leonarski_fandClaude Opus 5	e576184e2f	Docs: a quick start at the top of the rugnux page, and the indexing ambiguity written down ... The rugnux page opened with installation and reached its quick start around line 500 of 840, which is not where someone who wants to process a dataset looks. It now opens with four commands - the defaults, a reference MTZ, a model, and a pinned cell and space group, which is what people actually ask for - followed by the five files a run leaves and a few pointers. The old quick start keeps the detailed walkthrough under "Running rugnux", moved up to sit after the orientation sections. The indexing ambiguity had no prose anywhere, and neither did -z, which had one row of a table for four different jobs. A new section says what a reference MTZ does, what the ambiguity is, that it costs a rotation run an arbitrary frame and a serial run its CC1/2 outright, how to resolve it in each of the four cases, and that it is neither the enantiomorph nor twinning - the two things it is most often taken for. The three long reference pages carry a table of contents, from the MyST contents directive rather than a hand-written list, so it cannot go stale. The theme's sidebar already lists each page's H2 headings, so this adds the level below that and an in-page map; splitting the pages was the alternative and would have broken every anchor other documents link to. Two things the code says that the docs did not. --mode scale does not accept a reference MTZ on rotation data - the rotation scaler refuses it and the run stops - where the page offered it as one of the things to re-merge with. And CPU_DATA_ANALYSIS 10.9 still said stills use the reference as their per-image scale target, which stopped being true when stills were changed to scale against their own merge; the reference is their per-image ambiguity test and nothing else. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Vi1gV6Z45aZL5wLwe85Ksn	2026-08-26 20:04:45 +02:00
leonarski_fandClaude Opus 5	f7cb701f43	rugnux: let --model settle the indexing of the reflections it writes ... ValidateAgainstModel was called after WriteReflections, so the two relabelings it makes - the change of hand where the data were merged in the model's enantiomorph, and the alternative indexing it picks by R-free where no reference MTZ had already fixed it - reached the R-factors, the maps and _maps.mtz and nothing else. The .mtz/.cif/.hkl beside them kept whichever indexing the merge happened to land in, so a file whose maps came from a model could not be refined against that model without being reindexed first. Validation now runs before the reflection files are written and returns the operators it applied. AdoptModelFrame puts the merged reflections through them with a proper ASU reduction - ReindexReflections only relabels, which is all its scoring callers need - and the Bijvoet halves follow the Friedel sign of that reduction. The integrated observations are relabelled too, so --export-unmerged describes the same indexing as the merged files rather than a second one. change_of_hand_op is the inversion, so adopting a model's hand exchanges I(+) and I(-). On a tetragonal crystal whose enantiomorphic pair share their whole absence pattern, the search picks one of the two arbitrarily, and the exported anomalous differences were the wrong way round whenever it picked the other member from the model's. The written space group follows the hand, and so does the report that describes those files. The _process.h5 is deliberately left alone: its per-image reflections went to disk as they were integrated, and recording a group that did not match them would mis-merge on a later --mode scale. Nothing is lost - an enantiomorphic pair has the same Laue class and the same absences, so it merges identically either way. Serial stills could not use a model for this at all: each crystal is indexed in its own hand, so by the time there is a merge to fit a model to, the hands have already been averaged together, and reindexing the merged result as a whole cannot separate them again. ModelReferenceIntensities computes |F_model|^2 from the structure - Fcalc plus a flat solvent term at the standard constants, which are not fitted because there are no observations yet - and hands it to the per-image resolver that a reference MTZ already drove. It needs the cell and the group up front, which serial indexing wants anyway. Measured on a serial dataset in a merohedral trigonal group, at a fixed resolution limit so the shells match: CC1/2 better in 8 of 10 shells (79.7 to 82.5 overall), R_meas better in 9 of 10 (111.1 to 104.7), ISa 1.11 to 1.20, and R-free against a structure the merge never saw 0.393 to 0.375. The ambiguity probe now logs the runner-up R-free as well as the winner. On the same data the margin is 0.016 when the hands are mixed, where the two global indexings are tied because both are already inside every reflection, and 0.193 once they are not - the difference between a decision and a coin toss, which the old single number hid. The warning about an unresolved ambiguity no longer fires when a model will resolve it, and names the flags that would; and the summary line no longer offers the adopted group as its own alternative, which it did once --model had moved the run onto the member the search had listed as the alternative. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Vi1gV6Z45aZL5wLwe85Ksn	2026-08-26 20:04:02 +02:00
leonarski_fandClaude Opus 5	c8b05295c6	Version 1.0.0-rc.164 ... Runs update_version.sh, which regenerates the C++ server model, the TypeScript frontend client and the python client from the OpenAPI spec. That also propagates the space_group_number bound raised to 230 in the previous commit, so the generated clients stop rejecting cubic space groups before the request is sent. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Uwv9ScHtDH6g8tYgfSuApo	2026-08-26 17:00:06 +02:00
leonarski_fandClaude Opus 5	03dd28f40b	Changelog: the calibration outcome, the initialize wait and cubic space groups ... Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Uwv9ScHtDH6g8tYgfSuApo	2026-08-26 16:58:12 +02:00
leonarski_fandClaude Opus 5	c29dd67b5f	Broker: stop reporting a failed calibration as a successful one ... Every calibration step signals failure by calling SetState and returning normally - none of them throws, so none reached the catch in CalibrateDetector. The unconditional SetState(Idle, "Calibration sequence done", Success) after the try block then overwrote all of them. /cancel during a JUNGFRAU pedestal therefore left the broker Idle and apparently ready to measure while holding a truncated G0 and default-constructed zeros for G1/G2, and every subsequent run was silently mis-converted with nothing in /status to show it. The genuine failures - "Pedestal not collected properly", "Mask not collected properly" - were hidden the same way. The steps now return whether they succeeded, and the sequence reports success only if they all did. A cancellation or a failure leaves the state Inactive with Error severity rather than Idle or Error: the calibration is undefined, so the detector has to be initialized again, which is what Inactive means everywhere else in the machine. The exception path joins them, since a throw mid-sequence leaves the calibration no better defined. Cancelled pedestals were already Inactive but carried Warning severity, which reads as an advisory. CalibrateJUNGFRAU now abandons the sequence at the first failure instead of collecting G1 and G2 on top of a G0 that was never measured - the cancel path already behaved that way - and ConfigureDetector is skipped when there is no calibration to operate with, a cancelled sequence having left the detector mid-abort. Both error paths that end an Initialize now notify the condition variable. The state has left Busy, but without the notification a client in /wait_until_running slept out its whole timeout - up to an hour, if it asked for one - before noticing a failure that had already happened. Separately, dataset_settings.space_group_number allowed 1..194 in the OpenAPI schema while the broker accepts 1..230, so every generated client's validate() rejected all 36 cubic space groups before the request left. The regenerated clients follow in the version bump. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Uwv9ScHtDH6g8tYgfSuApo	2026-08-26 16:58:03 +02:00
leonarski_fandClaude Opus 5	a6a715703f	Broker: report a failed asynchronous start instead of a timeout ... An acquisition started with async_start returns from /start before the measurement thread has run, so a failure there had no caller to raise it to. MeasurementThread stored it in start_exception, but only the synchronous branch of Start() ever read it. The ordinary-failure path - a writer refusing to overwrite an existing file, say - sets the state to Idle rather than Error, and Idle is what wait_until_running_post maps to 504 "timeout, need to restart". So the one case the async workflow exists to report came back as a timeout with an empty body, and the writer's message was dropped. /wait_till_done was worse: Idle is its success case, so it answered 200 for a run that never started. Only a critical detector fault, which leaves the state at Error, was reported at all. The wait functions now rethrow start_exception, so both endpoints produce the same 500 and the same message as a synchronous start. rethrow_exception does not consume the exception_ptr, so repeated calls all report the same failure. It is cleared by every entry point that begins new work - Start (before ImportDatasetSettings, which can throw), Initialize, Pedestal, LoadDetectorSettings, SetDarkMaskSettings - so a pending failure is never attributed to the operation after it. The synchronous branch no longer clears it, so a wait call made after a failed /start reports the failure rather than an apparent timeout. wait_until_running_post and wait_till_done_post drop their timeout == 0 special case, which called GetStatus() directly and so bypassed the rethrow: ?timeout=0 returned 200 from /wait_till_done where ?timeout=1 returned the error. wait_for evaluates the predicate before expiring, so the state reported is unchanged. JFJochReceiverService::Start clears the receiver status when the start fails. JFJochReceiver's constructor sets progress to 0 and a zeroed status before the throw, and nothing cleared it, so /status reported Idle with progress 0 - a stalled acquisition, to the frontend - and /statistics reported an all-zero run that never happened, until the next start overwrote it. Its catch widens to std::exception, so a non-JFJochException gets the cleanup and the logging it skipped before. Nothing else is left dirty by a refused start: the receiver keeps its null receiver and Idle state, PrepareAction only resets counters (the FPGA is armed in StartAction, in a thread launched after the start message goes out), and SendStartMessage precedes every std::async in the receiver constructor. The test starts four more times afterwards, one of them a complete acquisition with no re-initialisation in between. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Uwv9ScHtDH6g8tYgfSuApo	2026-08-26 16:13:53 +02:00
leonarski_f	dd67cffde6	Docs: bring the release notes and the rugnux page up to rc.164 ... The changelog section had grown to 22 entries written from the commits rather than for a user. Collapsed to 13, each saying what is gained before what changed, with related work merged - the six anisotropy entries into one, five space-group entries into two, five integration-radius entries into one - and four things added that had no entry at all: the packaging split, the statically linked cuFFT, the Ceres back-end drop and REPORT_VERSION reaching 3. CPU_DATA_ANALYSIS gains 9.5, the adaptive integration radius: the r80 measurement, the clamp, the constant-ring-area r3, the convergence test, why it applies to the final pass only and the density fallback. Three passages there had gone stale against the code: 13.1 still described the I/sigma quantile fallback that b90fcfb98 deleted, and 13.5 said the gate tests delta_B when it tests delta_B_linear and that the high-symmetry caution fires wherever the Laue class leaves one free direction, which 0da593b32 narrowed. RUGNUX gains an Installation section - there was no page anywhere saying where rugnux comes from - a synopsis, a worked first run naming the files that actually appear and the report keys to grep, and sections on the unmerged export and on diffraction anisotropy. Its report section list was one section behind: anisotropy is 9, warnings is 10. The packaging change reached further than the changelog implied, so the pages describing what a release ships were corrected too: the viewer tarball no longer carries rugnux or the two developer utilities, the Linux archives link cuFFT statically rather than shipping it beside the binary under an $ORIGIN rpath, the aarch64 archive has a higher glibc floor than the RHEL 8 ones and is untested on hardware, the archives unpack with no top-level directory, and the notices live per package under share/doc/jfjoch_<component>. The RHEL 9.5 vm_flags workaround in FPGA_PCIE_DRIVER is obsolete and now says so.	2026-08-26 15:16:02 +02:00
leonarski_f	a67c52d8fa	Package rugnux as its own rpm and deb ... rugnux was a component of the jfjoch-viewer package, so getting the offline analysis CLI meant installing the desktop viewer, Qt and the XDS plugin with it. It links none of the hardware libraries and talks to no service, so a machine that only processes data should be able to install it alone. It is packaged as "rugnux", not "jfjoch-rugnux": the binary, the release tarball and docs/NAMING.md all call it that, and it is what a user types. Overriding the component's package name is the only way to drop the CPACK_PACKAGE_NAME prefix. /usr/bin/rugnux moves between two packages that both continue to exist, so the declaration has to be a bound on the OLD viewer rather than an Obsoletes - obsoleting jfjoch-viewer would uninstall the viewer. rpm gets Conflicts, deb gets Breaks+Replaces so the two stay co-installable from here on. rpm rewrites "-" to "_" in a package version (an installed release reads 1.0.0_rc.160), so the bound is built with the same substitution; spelled 1.0.0-rc.164 the comparison would silently never match, which is the failure mode this kind of guard usually has. Verified by building rpms from a project mirroring these settings: the package comes out named rugnux at 1.0.0_rc.164 carrying /usr/bin/rugnux and its notices, the jfjoch package no longer carries rugnux, and "rpm -i --test" against the rc.160 viewer installed on this workstation reports the intended dependency conflict rather than a raw file collision - which is what lets dnf resolve it by upgrading the viewer in the same transaction. The deb side is checked against CPackDeb.cmake, which supports NAME, BREAKS and REPLACES per component, but no .deb was built: this host is RHEL. CI needs no change; the upload step globs *.rpm and *.deb.	2026-08-26 15:15:44 +02:00
leonarski_fandClaude Opus 5	abb61e2708	Unmerged export: carry the sort key with the part here too ... SumRockingEvents assembles rocking events for the unmerged MTZ through the same indirect comparator the anisotropy diagnostic had, on a larger array - it has neither the scaled-image test nor the usable() filter in front of it. It is latent, since --export-unmerged is off by default, but it is the same defect and it is a mechanical fix. Same treatment: the key travels with the part, plus an exact reserve. p_unmerged.mtz, p_unmerged_partials.mtz and p.hkl are md5-identical across eight runs on two crystals. With the export on it is worth about 0.9 s on a seventeen-million-partial run. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-26 14:11:56 +02:00
leonarski_fandClaude Opus 5	0e6ece3c38	Anisotropy: assemble only the reflections the floor actually reads ... BuildObservationCells strides whole ASU clusters down to MAX_CLUSTERS = 20000 and keeps 1.4% of what it is handed - so the assembly before it sorted and summed every integrated partial in the sweep to throw 98.6% of the result away on the next line. The comment there says the striding "costs nothing and bounds the work"; it bounded it after the expensive part. Sample first instead: keep a partial iff a splitmix64 hash of its ASU key falls in the low one part in 2^n. Whole ASU clusters are mandatory rather than convenient - the cluster-robust sandwich sums one score per cluster, and the forbidden-direction signal IS the contrast between mates, so a raw-hkl sample would collapse that onto the independent covariance and inflate the floor. The hash rather than the key matters too: HKLKey::pack puts h in the low bits, so masking the key directly would select lattice planes instead of a sample. The rate comes from the partial count, not from merged.size(): the merged list is resolution-cut, and taking the rate from it made the first version never fire at all on the crystal it was written for. One part in 2^n of the partials is one unique reflection in 2^n, so the count already computed for the reserve is the right one. DELTA_B is unchanged by construction, not by luck. AnalyzeAnisotropy touches the unmerged observations in exactly two places - an empty test and MeasureSystematicFloor - so the tensor, the shape verdict and the directional limits come from the merged list alone. Over the battery: 0 verdict flips of 38; DELTA_B, DELTA_B_LINEAR, SHAPE, FREE_DIRECTIONS and the D_MIN keys differ on none of the 38, byte-identical rather than within noise; every reported key identical on 26; the mmCIF diff is exactly _reflns.jfjoch_aniso_floor and _significance; no caution appears or disappears anywhere. The spread those two keys move within was measured rather than assumed, and re-running cannot measure it because the code is deterministic. The shipped code already samples - by striding cluster order - so moving the phase of its own stride gives the sampling spread it has always carried. Against that control the change moves the floor less: ratio range 0.803-1.481 against 0.497-1.343, geomean 1.031 against 0.941. The gate therefore did not get easier to trip - the floor's geomean moves +3.1% here against -5.9% for the phase control, the crystal nearest the gate is not sampled at all and is bit-identical, and the two sampled crystals nearest the gate both move away from it. N_OBSERVATIONS goes up, not down, because a smaller pool lands the downstream integer stride slightly above the cluster cap. The ASU reduction is 14-45 ns a call in isolation, which nearly sank the design; in place it is free, because it overlaps the memory stalls of the Reflection stream it walks. The 24 crystals below the sampling cap run the shipped algorithm plus the reduction and cost +1.79 s in total, median +0.04 s. The block that introduced this measures 8.07 s before and 1.97 s after, which is 5.74 s off the largest crystal (-12.3%) and -11.9 s of anisotropy time over the battery. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-26 14:11:56 +02:00
leonarski_fandClaude Opus 5	62f0f6472d	Changelog: say what the anisotropy sort actually cost ... It was about eleven seconds on the largest sweep, not minutes. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-26 12:54:05 +02:00
leonarski_fandClaude Opus 5	e332aaf28c	Space-group search: read the presence cut on counting significance ... present_i_over_sigma is meant to say "this reflection is really there". The merged I/sigma is not that quantity. The merge carries the error model's intensity-proportional term, sigma^2 = a*sigma0^2 + (b*I)^2, so I/sigma saturates - at ISa*sqrt(n) for a reflection observed n times, and at ISa exactly for one observed once. Above that knee it stops rising with the intensity. Measured over the battery's 76 search merges: the median I/sigma of the top E^2 decile sits at 0.81 of ISa, and on the weakest merge the decile profile reads 1.58 1.61 1.63 1.64 1.64 1.65 1.65 against an ISa of 1.70 - flat to three digits, log-log slope against E^2 of 0.008. Reflections an order of magnitude apart in real intensity read the same number. So one constant demands between 2.16 and 11.91 in counting significance depending on the crystal, and the fraction of a merge clearing it runs from 3.1% to 98.8%. Convert it once instead. For a reflection observed once sigma_counting^2 = sigma^2 - (b*I)^2, so I/sigma_counting >= T is exactly t >= T/sqrt(1+(T/ISa)^2). That cut lies strictly below ISa for every ISa, so it is always reachable by the reflection the ceiling binds hardest, and it is within 1% of T on any merge with ISa >= 21, so a healthy merge is left where it was. Multiplicity is taken as 1 deliberately rather than estimated, for the same reason. The quantile fallback goes with it. Its comment claimed to be inert on the battery; it fires on 4 of 76 arms, and on one of them it relaxes the cut BELOW the nominal value because that merge is bimodal. A cap on a statistic is not a substitute for measuring the right statistic. Two comments in the tree still described a merged sigma floored at b|I|, removed in 72efb75a8 before rc-161. Both corrected; that stale claim is what made this look like a different bug. Battery, both arms, against a control floor of exactly zero: space groups 35/38 before and after, the same three crystals differing from the reference, all 380 shells identical and all 38 merged mmCIFs byte-identical. It is live rather than dead code - the pass_cc population moves on 45 of 47 arms and 212 of 314 operator correlations move, with 0 of 314 verdicts changed. The weakest crystal's single 2-fold goes from CC 0.489 on 1131 pairs to 0.597 on 4822, widening its margin over the threshold by 57%. Two things this does not fix, both quantified in the work behind it. The conversion is monotone, so it corrects the threshold but cannot restore the ranking the (b*I)^2 term already destroyed - that needs a counting-only merged sigma and touches the CUDA merge kernel. And one crystal's gate still admits 98.8% of its merge with a slope of 0.037, discriminating nothing; the instrument for that is E^2, which needs min_operator_cc re-derived first. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-26 12:43:04 +02:00
leonarski_fandClaude Opus 5	278f8e3d73	Anisotropy: carry the sort key with the part, as the merge's ingest does ... ScaledObservations assembles every integrated partial into rocking events before the tensor is fitted, and sorted them through a pointer. On the largest sweep that is 29.1 million parts spread over about 2.5 GB of 88-byte records against a 32 MB L3, and the comparator dereferenced one of those pointers on every one of roughly 660 million comparisons. Single-threaded, once per run, at the end of a run whose image loop uses sixteen threads and a GPU - and for a diagnostic that corrects no intensity and removes no reflection. It was 8% of one run, 12%, 15% and 16% of others, and 19% of the largest. The fix is the idiom this repository already uses for this exact sort: RotationScaleMerge's ingest sorts the same partials on the same key through a narrow record and its header says why. ScaledObservations was the one place that read the key back through the pointer instead. The key now travels with the part. Twelve lines, no bit-packing, and a reserve of the upper bound so the growth chain stops copying a few hundred megabytes on a large sweep. Ties are real and had to be handled rather than argued away: the predictor emits both Ewald intersections and near the blind region both land on the same frame, so one crystal has 7424 tied adjacent pairs, 3778 of them in reverse arrival order. The comparator keeps the same four values in the same order, so introsort - whose every branch is decided by comparator outcomes at positions and never by element size - makes the same comparisons and the same swaps and leaves the same permutation. Checked rather than asserted: a hash of the sorted permutation of all 29.1 million parts, a hash of the returned vector's raw bytes, and the md5 of the whole .cif all match on eight crystals, each first run twice on the baseline as a determinism control. The sort is 1.7-2.1x faster and the function 1.5-2.0x, which is 6.7 s of single-threaded critical path over those eight crystals and 10.8% of total wall clock over six timed warm and interleaved. A wider element costs 7% in the grouping pass that follows. A 24-byte variant that indexes back instead was built and is marginally faster to sort and slower overall, so the plainest version is also the fastest. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-26 11:35:34 +02:00
leonarski_fandClaude Opus 5	c4f4f7e28f	Stills: run the background ring to 14 px instead of 12 ... The reported sigma carries the background ring mean's own error as (dI/dbkg)^2 * bkg/n_ring, and the stills ring holds only 244 pixels at r3 = 12 against the rotation default's 408 - so that term is a larger share of the variance here than anywhere else in the program. r3 = 14 takes the ring to 416. What normally stops a ring being widened is crowding, since a neighbour inside the annulus is excluded from it. Stills barely crowd: neighbour occlusion is 0.000% at both radii on six of the seven datasets scored and 0.721% -> 0.678% on the densest, against most reflections having a neighbour within 13 px on rotation. Rotation is left alone at 4,6,13, where the ring already wins by a factor of several. Measured with the new stills harness over six datasets and 72 shells, 10000 images each, resolution range pinned so both arms share shell edges, against a control floor that is bit-identical in every column: <I/sigma> +1.23% median over the 56 signal-bearing shells (44/56) R_meas -0.37 points (39/56) CC1/2 flat (29/56) obs flat R_meas is the number to read here. <I/sigma> improving when the ring is widened is half mechanical - a better background estimate lowers sigma by construction - whereas R_meas has no sigma in it, so it moves only if the intensities themselves got better. A prediction from ring pixel counts alone, made before the run, was 1.6-2.7%; landing at 1.2% with the profile-fit weighting in the way is the mechanism behaving as expected. The larger and more consistent effect is the opposite of the risk this was checked against: reflections discarded for want of a background ring fall from 2.53-2.88% to 1.87-2.25% on all seven datasets, because a wider ring reaches past the module gap that starved the narrow one. Against it: CC1/2 and observation count are flat, and the gain reverses below <I/sigma> of about 4 - median -0.4% and -0.6% in the two weakest bands. Roughly a fifth of that is background curvature, which --background-radial recovers; the rest is not explained. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-26 11:26:43 +02:00
leonarski_fandClaude Opus 5	39a0b067a4	Add a stills validation harness, the analogue of rugnux_vs_xds.py ... rugnux_vs_xds.py gates every rotation change in this project. Nothing gates a stills change, so until now one could not be validated at all - which is why the background-ring width below had to be measured before it could be argued about. The rotation harness does not transfer. A stills dataset is one file of 100k-500k images with no per-crystal reference, the space group is known in advance and never in question, and what a change moves is the merge. So this asks a different question - did this make stills data better or worse - by running rugnux over the same fixed image subset under two or more argument sets and tabulating the merge per resolution shell. Three things it does on purpose. It pins the resolution range per dataset so both arms share shell edges: without that the automatic cut-off moves between arms and the columns are not the same shells, which happened on two of seven datasets. It fixes and prints the image subset, contiguous rather than strided because a stride turns one sequential read into ten thousand seeks. And --repeat measures the control floor, which on six of seven datasets is bit-identical in every column of every shell. It reads the stable interfaces - the report's KEY= value lines and the mmCIF _reflns block and _reflns_shell. loop. The one console-log number, how many predicted reflections lost their background ring, is labelled as such; it is there because it is the only place the price of a wider ring is counted. A CrystFEL stream can be scored alongside as an optional reference, keyed on the global image serial number - Event: //N restarts at zero in every file and silently multiplies the count. No dataset list is shipped. A dataset directory name identifies a sample, and so does a run label or a pump-probe parameter in a filename, so the table committed here is a template carrying the reasoning and no paths. A real one belongs in a config kept outside the repository, which is why --config is required and has no default. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-26 11:26:02 +02:00
leonarski_fandClaude Opus 5	d987bd6178	Space-group search: record what the E^2 shell count does on a small merge ... The shell count is order.size() / 100 in integer arithmetic, so a merge of fewer than two hundred reflections gets a single shell and E^2 becomes I divided by one global mean. That is harmless for the thing E^2 was introduced for - the operator correlation is a Pearson coefficient and is invariant to a common scale, so it lands on exactly the value raw I would have given. It is not harmless for the overlap cap, which then rejects reflections by their intensity against the whole merge rather than against their own resolution shell, and so cuts the low-resolution end and spares the high. No behaviour change; a merge that small has already failed for other reasons. This is here so the next reader does not have to rediscover that the normalisation quietly switches off at the bottom of the range. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-26 10:29:58 +02:00
leonarski_fandClaude Opus 5	00c27584cb	Spot width: stop doing obviously redundant work in the pixel loops ... None of this is worth its speedup - the routine is 0.5-0.8% of the pre-scan's cycles on two independent profiles, and the whole change is 0.9 ms per data set. It is worth having because the code was doing work that has no reason to exist. The isolation grid was a vector<vector<uint32_t>> over ISOLATION_PX cells: on a 4148x4362 detector that is 23244 std::vector objects constructed, heap-allocated and destroyed per image for a structure that is read once. It is now a counting sort - one offset array, one index array. This was the largest single item and it is not a pixel loop. The encircled-flux curve added every pixel into every bin at or beyond its own radius, about 7.5 adds per pixel, which sums the same aperture R_MAX/2 times over. Each pixel now lands in the one bin its radius falls in and the curve is the running total. The bins are double where the running totals were float, so the result is more accurate, not merely faster. No square roots remain in the pixel loops. The isolation and beam gates compare squared distances, and the radial bin is a table lookup over the 197 squared distances the aperture can produce. That is the same bin, not an approximation: floor(sqrt(floor(y))) == floor(sqrt(y)) for every real y >= 0, because k*k is an integer, so the table recovers ceil(sqrt(rc2)) exactly once the perfect-square case is separated out. The disks are also walked as disks rather than as their bounding boxes - constexpr per-row half-widths - which takes the background pass from 1681 to 1257 pixel visits per spot. Verified over the rotation battery: r80 identical to nine significant figures on 37 of 37 measurable crystals, the 38th unmeasurable in both arms, and the chosen r1 identical on 38 of 38. The pass feeds nothing but r1 into the run, so merged output is unchanged. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-26 10:25:17 +02:00
leonarski_fandClaude Opus 5	1bb4cecbd1	Spot width: measure on a growing sample and stop once it settles ... The pre-scan measured the spot width on all 60 frames of its sample every time. The radius that measurement feeds is a three-way choice - R1ForWidth moves only where 2*r80 crosses 4.5 and 5.5 - and 29 of 37 measurable crystals sit more than 0.29 px clear of both switches, so most of the sample is spent confirming a bucket the first few frames already picked. Measure instead on a growing share of it - every eighth frame, then every fourth, every second, all of it - and stop at the first tier whose answer has settled: within 0.40 px of what the smaller sample said AND 0.25 px clear of both switches. Both conditions are load-bearing. Clearance alone loses the crystal whose r80 is 0.07 px from a switch, because its small samples read across it; the step test alone lets a sample settle on a switch and stop there. Both bounds sit interior to a two-dimensional region that is right on 38 of 38, and every candidate was re-scored at all eight phase offsets of the tier ladder. The tiers are sized in worker-rounds rather than frames: a first tier of five frames occupies eight workers as long as one of eight does. A {12,4, 2,1} ladder measures 11% fewer frames than {8,4,2,1} and is 11% slower. Over the rotation battery this reads 1215 of 2280 frames - 21 crystals stop at 15, 4 at 30, 13 still run all 60 - and the chosen r1 is identical on 38 of 38, as is the beam-stop mask the reordered loop also touches. The pass feeds nothing else into the run, so every merged intensity is unchanged by construction and no battery is required. Cost over the battery goes 15.6 s to 10.1 s, median 0.18 s to 0.14 s per data set. Note for anyone optimising this further: the measurement itself is 0.54% of the pre-scan's cycles. The cost is the decode, preprocessing and spot finding each frame needs before it - 64% of the pass - because the beam-stop projection decodes on the GPU and never materialises the frame on the host. Cutting frames is the only lever short of harvesting the width from the two-pass run's first GPU pass. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-26 09:55:34 +02:00
leonarski_fandClaude Opus 5	7e3ab8150d	Integration: widen the radius for the final pass only ... 48008e144 set the integration radius from measured spot width, and on one crystal that cost 21% of the indexed frames. The cause is not the indexer. The geometry pre-pass integrates, post-refines the detector distance and beam from what it integrated, and discards the intensities. PostRefine takes its positions, its weights and its reflection set from the integrator, and the observed position is a raw first moment over the signal disk with the background still in it. A flat background contributes nothing to the numerator, because the disk is centred on the prediction, but it adds n*b to the denominator - so every measured offset is pulled toward its prediction by I/(I+n*b), and n goes from 50 pixels at r1 = 4 to 113 at r1 = 6. A wider disk under-corrects the geometry. Measured: 225.978 mm against 225.944, and a slightly worse held-out residual. That is the entire difference the pre-pass hands on: 33 microns of distance and 0.02 pixels of beam. It is enough because that crystal's metric is 0.54 degrees off orthorhombic, so the de-novo Bravais choice sits on a knife edge - scanning the beam in hundredth-pixel steps flips it back and forth in islands, and both sides are bit-reproducible. Snapping the cell to 90 degrees costs a contiguous 66-degree stretch of the sweep, which is where the frames go. So the pre-pass now keeps the radius the run started with and only the final pass integrates at the measured width. Pass 1 becomes bit-identical to a fixed-radius run, so the geometry it hands on is too, by construction rather than by tuning: on all twelve crystals the rule moves, the post-refined distance and the pass-2 validation frame count match the fixed-radius values digit for digit. On the crystal that regressed, the indexing rate goes 0.7900 to 1.0000, observations up 30.1%, multiplicity 5.22 to 6.68, and low- resolution R_meas 13.1% to 10.7% against XDS's 10.8%. Against the right reference - the rule off, same lattice, same geometry, matched indexing rate - the widened radius on that crystal is better in 10 of 10 shells on R_meas and 10 of 10 on CC1/2. It looked worse against the shipped arm only because that arm merges a fifth fewer frames, and dropping the hardest part of a sweep flatters a pooled statistic. Taking the position centroid over a fixed aperture regardless of r1 was tried and does not work: the intensities, the sigmas and the surviving reflection set carry the perturbation too, and the geometry moved further from the baseline, not closer. Battery: space group identical on all 38 and 35 agreeing with the reference in every arm, merged intensities byte-identical on the 26 crystals the rule does not move, over a baseline reproducible to zero. No runtime cost. The density guard moves with it and now reads the final pass's own count. Exercising its re-run branch with a lowered bound turned up two reporting bugs, fixed here. Not fixed, and worth its own task: that crystal is still one hundredth of a pixel from losing a fifth of its data, because the indexer computes the unconstrained cell for exactly this comparison but only scores it once the constrained one has already failed outright. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-26 01:58:43 +02:00
leonarski_fandClaude Opus 5	64957d5a5f	Space-group search: record what min_pairs_per_operator is actually worth ... Comment only; the constant stays at 20. f6bfa5462 moved min_operator_cc to 0.30, which is close enough to the null of a sparse operator that the pair minimum deserved measuring rather than assuming. Measured, over 38 crystals and 142 (crystal, pair-count) points, the null of the normalised operator correlation has mean -0.02 to +0.05 and standard deviation 1.08/sqrt(n), flat from 20 pairs to 5000. Its tail is the part worth writing down: log10 P(null CC >= 0.30) = -1.03 z + 0.69, residual sd 0.14 decades One decade per standard deviation, where normal theory gives about five. So a false operator at 20 pairs clears 0.30 on 12.4% of draws, and any calibration of this gate that reasons from 1/sqrt(n-3) with a normal or Fisher-z tail is optimistic by one to two orders of magnitude. It does not bite where the decision is made. Over 314 candidate operators on 36 crystals the sparsest has 520 pairs and none is below 500; the weakest confirmed operator sits 9.1 sigma above its own null and the strongest rejected one 42.7 sigma above. Nothing passes on noise. The search's own <I/sigma> cut is what keeps that null flat - reconstructing the same crystals from an unfiltered merge reproduces a null floor of 0.10 to 0.20, which is where the "false CC rises at low pair count" impression came from. That describes a shrinking merge, not a sparse operator. A minimum of 251 pairs would buy a per-operator false rate of 1e-3. It was built and rejected on measurement: SearchSpaceGroup runs twice, once on all observations, which decides, and once on a Lorentz-filtered merge, which only reports - and no log prints the second arm's pair counts. Genuine operators fall to 98 pairs there, so a floor of 251 empties a conjugacy class on one crystal and makes the report say its filtered merge supports triclinic, about a merge whose own correlations put every one of those operators 9 sigma clear at 0.91 to 0.97. Any floor above about 150 does that; any below about 103 is barely better than 20. A count floor rejects on pair count however decisive the correlation is, which is why the shape is wrong rather than the value. The comment records the law, the rejected value, and the form that would work if this is ever revisited - a significance floor rather than a count floor. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-26 01:44:32 +02:00
leonarski_fandClaude Opus 5	f6bfa54624	Space-group search: score operators on normalised intensities ... Symmetry operators were scored by Pearson correlation on raw merged intensities. Both members of a symmetry pair sit at the same |s|, so the resolution fall-off is variance the two arms share exactly, and it inflates the correlation of true and false operators alike. The clearest demonstration is the test this commit adds: a synthetic data set with no symmetry at all - a radial fall-off times an independent per- reflection factor - is assigned point group 432 by the shipped code, with all 23 rotations confirmed at 0.632 to 0.656. The existing suite passes identically before and after, because nothing covered this. The new case fails 64 of its 100 assertions on the old scoring and passes on the new. On real data the same effect had the gate leaking: on one cubic crystal three pseudo-symmetric operators scored 0.506 to 0.517, above the 0.5 bound, so they were confirmed and 432 had to be refused further downstream by the twin-law and systematic-b guards. Scored on E-squared they read 0.283 to 0.298 and exactly the eleven genuine rotations of 23 are confirmed. The normalisation has to be over the reflections the correlation actually pairs. Reusing the existing normalised array is worse than doing nothing: it is normalised over the set the absence tests use, whose surviving fraction is itself resolution-dependent, and the coupling to the resolution cut rises from 0.086 to 0.262 against a raw baseline of 0.086. Normalised over the paired set it falls to 0.023. The twin-law H statistic keeps its own vectors on raw intensities. It shares the pair arrays with the correlation, and normalising in place moves it by up to 12% against a bound whose window is 5.5% wide. Verified rather than assumed: two instrumented binaries print the same H to twelve significant figures while the correlation differs. min_operator_cc goes 0.5 to 0.30. Normalised correlations run lower, and the observed window on rugnux's own search merges is 0.298 to 0.351; 0.35 is too high, because one crystal's weakest genuine operator reads 0.351. The headroom between a crystal's weakest true operator and its own measured false -operator floor widens on 14 of 14 crystals, median 0.430 to 0.619, and the worst operational margin goes from 0.031 to 0.051. Battery, twice, against a baseline reproducible to zero: the space group is identical on all 38 crystals, per-shell merging is 0 better and 0 worse across all 380 shells, and the merged mmCIF is byte-identical on 38 of 38 - on the 12 crystals whose integration radius now adapts as well as the 25 that do not. The arm is live rather than inert: all 313 operator correlations move while every pair count and every H value stays bit-identical, and on one cubic crystal three operators that raw intensities confirmed are rejected, with the space group unchanged. Following Padilla and Yeates (2003) Acta Cryst. D59, 1124-1130 for why a resolution-normalised statistic is the right one for a symmetry test. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-26 00:27:13 +02:00
leonarski_fandClaude Opus 5	4e6eb18d93	Integration: fall back to the fixed radius on a pattern too dense for it ... 48008e144 widens the signal radius on crystals with wide spots. On one battery crystal - simultaneously the widest-spot and among the highest in mosaicity - the wider radius left its neighbours' background rings with too few clean pixels and cost 28.5% of its observations. Pass 1 now measures how often that happens and, above a bound, hands pass 2 the settings from before the pre-scan widened them. The obvious quantity does not work. On the total rate of reflections dropped for a starved ring, the losing crystal reads 4.08% and the rule's four biggest winners read 1.89-2.04% - and a crystal at the shipped radius reads 2.37%, above all of them. Re-running the winners at r1 = 4 shows why: they read 2.20-2.32% there too, and widening moves them down. That floor is module gaps, the beam stop and the resolution mask, which are properties of the detector and do not move with the radius. So the counter separates the two. A ring is neighbour-starved when it would have kept more than five pixels but for the pixels a neighbouring reflection's signal region occupies. That is exact rather than estimated: the reflection mask marks the disk inside r2 and the ring is everything outside it, so a masked ring pixel always belongs to some other reflection's core. The separation goes from a factor of 2 to a factor of 13 - over the twelve crystals the radius moves, the rate is 0.000 five times, 0.001 three times, then 0.004, 0.235, 0.315 and 4.082 - and the bound is the log-space midpoint of that one gap, 0.0113, a factor 3.6 clear of the nearest measurement on either side. Predicted reflection spacing does not separate them at all: the losing crystal is 19th of 38, a winner sits at 21.9 px, and the loosest pattern in the battery starves 1.93% of its rings. Battery: the space group is identical on all 38 and the merged .hkl is byte-identical on 37, so it is inert wherever it does not fire. On the one crystal it fires on, <I/sigma> is up 18.3%, R_meas down 29.4%, observations up 6.3%, CC1/2 0.944 to 0.974, and its two empty top shells come back as numbers. Its indexing rate, refined distance, beam centre and cell are bit-identical between the two arms, so this is the guard and not the two-pass gate. The counters are a shared channel through both engines, summed across workers and logged once per pass; on the GPU it is one atomic add per dropped reflection. The profile-fit runaway guard reports on the same channel, which is the first measurement of its trip rate. This does not recover that crystal fully. With the adaptive radius on, pass 1 reaches a different lattice and pass 2 indexes 21% fewer frames - which happens before the measurement this guard reads exists, and is unaffected by it. At matched indexing rate the guard recovers 96% of the baseline's observations against 90.5% without it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-26 00:20:41 +02:00
leonarski_fandClaude Opus 5	0da593b32a	Anisotropy: say what was measured, and stop crying wolf ... Four reporting changes and a restored changelog line. The gate boundaries are unchanged - see below - and no merged number moves: .mtz and .hkl are byte-identical on two crystals, and REPORT_VERSION stays 3 because everything here is an added key or prose. A directional diffraction limit that is really the edge of the measured data was printed as if it were the crystal's. One crystal reported 1.09 / 0.99 / 0.99 A against a 0.994 A cutoff, so two of its three limits were the cutoff. A censored limit now prints with a "<" and sets ANISOTROPY_D_MIN_CENSORED. It fires on 4 of 28 crystals, and on two of those all three limits are censored, which means their reported directional spread was binning noise. The caution about a too-high symmetry assignment fired on every crystal with one deviatoric degree of freedom - every tetragonal, trigonal and hexagonal case, 17 of 38. A caution that fires on 45% of runs is noise. It is now conditional on the signature that actually indicates it, a large symmetry-forbidden signal with a gate that established nothing, and fires on 2 of 38: the crystal already on record as space-group unstable, and one other. The forbidden-direction z is now reported so the reader can see it; its battery median is 6.5. The verdict line quoted deltaB_linear while the headline reported deltaB, and the two differ - deltaB_linear is the larger on 12 of 31 crystals. It now writes out the arithmetic, says which number the gate tests, and says which to act on. The observation count the floor was measured on is reported, and the mmCIF verdict item carries its vocabulary like its neighbours. On the boundaries: they were calibrated against XDS-derived unmerged data, while production measures the floor from rugnux's own observations, and those disagree by 0.12x to 16.2x with 7 of 29 verdicts flipping. Re-measured on production input - by merging each cubic crystal in proper subgroups of its own Laue class, where the true anisotropy is exactly zero and every deltaB that comes back is manufactured - the false-positive rate is 24% at 2.0, 10% at 3.5 and 5% at 5.0. Each sits inside the published band read as its worst-case figure rather than its average. 3.5 maximises power minus false-positive rate across the grid; moving to 4.0 costs a real detection and reduces the false-positive rate by nothing. So the boundaries stay, and the "strong" band at 5.0 is a 5% statement on real data rather than the 0.5% its derivation suggested. The changelog entry for the diagnostic itself was committed with only its first line, having been extracted by a script that took one line of a four-line bullet. Restored. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 23:56:08 +02:00
leonarski_fandClaude Opus 5	48008e1447	rugnux: set the integration radius from the crystal's own spot width ... On rotation data the signal radius is now r1 = clamp(round(2*r80), 4, 6), where r80 is the 80% encircled-flux radius of the crystal's own spots. The background ring keeps its area (r3 = sqrt(r2^2 + 133)), so r1 = 4 is the shipped default bit for bit and 26 of the 38 battery crystals come out byte-identical. The width had to be measured somewhere new. rugnux already has one - shell_sigma2[].tan - but it is a second moment taken inside the r1 disk it would be setting, and it saturates at r1/2, so feeding it back measures the cap and not the crystal. SpotWidth instead measures encircled flux over an aperture fixed for the whole file (14 px, normalised at 8), in the pre-scan, from spots the finder already produces on the frames the beam-stop projection already reads. It touches no integrator output and runs before the first integration pass, so there is no loop, it costs no extra frame reads, and both passes - including the space-group search, which runs in pass 1 - see the same radius. A default run pays a median 1.9 s. k = 2 is not fitted. For a Gaussian r80 = 1.794 sigma, so r1 = 2*r80 is 3.59 sigma, where the truncated second moment recovers 0.990 of sigma^2. The new test checks the estimator returns 1.794 sigma on a known Gaussian. Battery, 38 crystals, both arms run twice: the space group is identical on all 38 and 35 agree with the reference in both arms. Per shell on the 12 crystals the rule moves, 6 win and 4 tie, with mean per-shell <I/sigma> up 30.6, 24.6, 15.8, 9.1, 8.0 and 5.1 per cent and R_meas down as much as 23.8. Runtime is neutral - 19m13s against 22m00s warm. One crystal is a real cost and is named in docs/RUGNUX.md with its workaround: an I222 case that is simultaneously the widest-spot and among the highest-mosaicity in the set loses 28.5% of its observations at unchanged completeness, because at r1 = 6 its predicted reflection density leaves the background ring too few clean pixels. No cheap guard separates it - its predicted spacing is mid-table, larger than five crystals that survive r1 = 12 - and the guard that would, on the measured drop rate out of pass 1, needs a diagnostic channel out of both integration engines and is not yet validated. This depends on 3ea120677: at the previous twin-law bound of 1.70 the wider radius costs one crystal its 422, refused on an H ratio of 1.73 even though every operator correlation confirms the point group. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 22:45:02 +02:00
leonarski_fandClaude Opus 5	db908c6ec1	_process.h5: record the change of basis, and the space group ... A _process.h5 was internally inconsistent whenever the space group re-seated the lattice. The per-image reflections and lattices go to file as each image is processed, but the conventional setting is only chosen afterwards, so the file kept pre-reindex indices beside a post-reindex cell. Measured on an affected dataset, max|d_file - d(hkl, stored cell)| was 18.6 A. --mode scale then compared each frame's lattice against the stored cell, found none of 1800 acceptable, rejected every observation and died in the merge with "resolution calculation failed". /entry/MX/reindexMatrix now carries M with hkl_cell = M . hkl_written, and the reader applies it, so everything it hands out is in the setting of /entry/sample/unit_cell. Absent means the identity, so a file written before this reads exactly as before. On the affected dataset M comes out [[1,1,0],[0,1,1],[1,0,1]], det 2 - the primitive-to-body-centred basis its volume ratio implied - and the same measure falls from 18.6 A to 1.8e-5. Writing the reflections in the final setting instead was rejected: the per-image writer is shared with the broker, which streams and cannot buffer a run; and h,k,l, predicted_x/y and the per-image lattice are one consistent statement about one image, which retro-editing the indices would silently break. Two things turned up while fixing it. There are three re-seat sites, not one - the space-group search's own centred-lattice test re-seats too, and logged nothing - so the matrix composes over all of them. And the space group itself was never written: it was set only on the arm that searches, while a two-pass rotation run reuses pass 1's group and takes the other arm, so the canonical file carried a cell but no group and --mode scale merged in P1. --mode scale now reproduces --mode mx on the affected dataset: same space group and cell, 39329 unique reflections both, 100% of reflections common, CC 0.99985, sum|dI|/sum|I| = 0.0081. The residual is three reflections in 11.09 M crossing an ice-band edge, because mx carries the integrator's d and scale recomputes it from the cell. An unaffected dataset is byte-identical in .mtz, .hkl and .cif. An older affected file still cannot merge - M is not recoverable from it - but now says so in 51 s, naming both cells and the -S/-C override to use, instead of failing inside the merge. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 21:21:55 +02:00
leonarski_fandClaude Opus 5	8fa1ab7b05	CI: make the artifact checks capable of failing, and of passing ... The rugnux tarball built and packaged correctly; the step that verifies it did not. Two shell mistakes, both mine, both of the same family. `! find /tmp/rgx -name 'libcufft*'` can never pass: find exits 0 whether or not it matched anything, so the negation always fails. That is what broke the x86_64 job after a successful build. The aarch64 checks were worse, in the way that matters. Piping a large producer into `grep -q` kills the producer with SIGPIPE as soon as grep exits on its first match, and `set -o pipefail` promotes that to the pipeline's status: on `cuobjdump --list-elf | grep -q sm_90` over a 225 MB binary it fails a check that should pass, and on `! ... | grep -q "x86-64"` the leading `!` inverts it into a PASS -- so an x86 file leaking into an aarch64 tarball, the exact thing that check exists to catch, would have been reported as clean. Both now capture each producer's output to a file and grep the file, with explicit if/exit rather than exit-status negation. Verified by running the checks verbatim against the real artifacts rather than only reading them: both tarballs pass, and the checks were confirmed to FAIL when they should -- an x86_64 file planted in the extracted tree is caught, and an architecture absent from the fatbin is reported missing. The toolchain file now comes from the checkout rather than /opt/cross in the image. It describes how to build this source, so it belongs with the source: baked into the image, the Eigen fix in the previous commit could not reach CI without rebuilding and re-pushing the image, and appeared to have no effect. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SQjneRUssfhi1k9rq8Ts3h	2026-08-25 21:21:11 +02:00
leonarski_fandClaude Opus 5	3175e65400	Space-group search: say what it tested, and what it could not ... Three reporting changes. None of them touches a decision: the merged .mtz, .hkl, .cif and _image.dat are byte-identical before and after on two test crystals, and the space group and cell are unchanged. REPORT_VERSION moves to 3 and one warning appears where the second change is working. The alternatives line was misleading. "Best space group: C2 or P21 or P2 (indistinguishable from these data)" sat forty lines below the run's single cell, which is C2's. P2 and P21 are primitive: their lattice is a sub-lattice of that one, their cell has half its volume, and their indices are not the ones in the written files. A user acting on "P21" got a group name with no cell, beside a cell belonging to a different group, with nothing saying so. The report now names the alternatives whose centring differs from the chosen group's, gives the volume ratio of the cell each implies, and says that adopting one means reindexing. It stays byte-identical when every alternative shares the chosen centring, which is every other case that occurs - the enantiomorphic and origin-ambiguous pairs, where one cell really does describe them all. It does not print derived cell constants: the primitive cell of a C-centred monoclinic is not P2's conventional cell, and deriving that is a reduction plus a per-group setting choice, which is more than a report line should carry. A centring the data could not test now says so. Prediction runs in P so the search can confirm a centring from the reflections it extinguishes, but when the indexer returns the primitive sub-cell those reflections are never predicted, and an absent count of 0 reads as "predicts no absences" when it means "none was measured". The search abstains correctly and the centring is then taken from the metric, but none of that reached the user. The candidate table gains a three-valued centring column and the report raises a warning where the metric decides it. No decision logic changed - the flag is two counts the search had already made, and nothing reads it back. The twin-law H is now reported for every operator, and the adopted promotion's ratio against its bound. It was previously visible only inside a refusal message, which is why recalibrating that bound recently required rebuilding the statistic from reference data rather than reading it out of runs we already had. The ratio is reported at the Stage A promotion where it is computed, not in the Stage B table, whose rows all share one point group and would have printed the same number on every line. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 21:04:12 +02:00
leonarski_fandClaude Opus 5	a4228b9c1d	tests: follow REPORT_VERSION to 2 ... 80e10f51b added an anisotropy section to the result report and moved REPORT_VERSION from 1 to 2, but left ResultReportTest asserting 1, so the [Diagnostics] tag has been failing on this branch since that commit. The assertion is the point of the test - a consumer greps that key - so it follows the constant. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 20:57:37 +02:00
leonarski_fandClaude Opus 5	491312f263	Fix the packaging split where it was only exercised on one configuration ... Three failures, all from validating the rugnux path alone and assuming the rest followed. viewer/CMakeLists.txt had an unbalanced ENDIF: removing the cuFFT bundling block took its opening IF(JFJOCH_CUDA_AVAILABLE) with it and left the closer behind, so every configuration that adds viewer/ died on "flow control statements are not properly nested" -- both Windows jobs and the viewer tarball. The cross toolchain could not find Eigen. CMAKE_FIND_ROOT_PATH_MODE_PACKAGE ONLY confines find_package to the target roots, and the ubuntu2404 image installs Eigen from source in /opt/eigen-3.4 rather than as libeigen3-dev, so it sat outside them. It is header-only, so serving it from outside the target roots is safe; the root is now listed explicitly. Static cuFFT is not available everywhere. The Windows toolkit ships no cufft_static.lib, so CUDA::cufft_static does not exist there and linking it fails at generate time. Condition on the target rather than the platform, so a toolkit that gains or loses the static library needs no further change, and restore the Windows DLL bundling for both products -- now in the top-level CMakeLists, since rugnux needs it too and does not add viewer/. rugnux.exe therefore ships beside cufft64_*.dll rather than alone; the Linux and cross artifacts are still one file. That condition also has to keep the JFJOCH_PORTABLE_ONLY half. Testing only for the target quietly moved the SERVER build onto static cuFFT as well, where every executable -- broker, tests, tools -- would then need the CUDA device-link step and would fail on an undefined __cudaRegisterLinkedBinary_* at link. Configure still succeeds, so nothing catches that until the link; the server build keeps libcufft.so exactly as before. Checked by configuring all four flavours in the image CI actually uses -- rugnux, viewer and server on x86_64 plus the aarch64 cross -- and confirming each links the cuFFT it should. The rugnux archives now also carry their target architecture, since that build produces more than one: rugnux-<version>-linux-x86_64-cuda13.tar.gz beside the aarch64 one. CMAKE_SYSTEM_PROCESSOR is the target's, never the build host's. The viewer is x86_64-only and keeps its existing name. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SQjneRUssfhi1k9rq8Ts3h	2026-08-25 20:53:49 +02:00
leonarski_fandClaude Opus 5	fd9e7bce1f	CI: drive the Windows rugnux build from cmd, as the viewer build already does ... The job used shell: bash, and the Windows runner has no bash on PATH, so it failed before running cmake. It also skipped the MSVC environment, which every cmake invocation on that runner needs: build-windows calls vcvars64.bat, located through vswhere, at the start of each step. Follow it exactly - cmd, the same vcvars preamble, -G Ninja, and cpack from inside the build directory - and keep powershell only for the upload, which is what build-windows uses there too. CMAKE_PREFIX_PATH drops the Qt entry and keeps C:/deps: JFJOCH_RUGNUX_ONLY is the portable subtree minus viewer/, so it needs Eigen and ZLIB and no Qt. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SQjneRUssfhi1k9rq8Ts3h	2026-08-25 20:12:55 +02:00
leonarski_fandClaude Opus 5	6a7404f03f	CI: upload the rugnux artifacts the way every other job does ... The three new rugnux jobs reached for akkuman/gitea-release-action@v1, which does not exist on this Gitea: actions resolve against gitea.psi.ch/<owner>/<repo>, so the runner tried to clone gitea.psi.ch/akkuman/gitea-release-action and failed. That happens while preparing the workflow, before any step runs, so all three jobs died immediately without building anything. Every other job uploads with gitea_upload_file.py and the release token, so use that: bash on the Linux jobs, powershell on the Windows one, matching the viewer tarball and installer steps they sit next to. The Linux archives are renamed .tar.gz -> .tgz first, as the viewer archive already is. actions/checkout is now the only external action the workflow references. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SQjneRUssfhi1k9rq8Ts3h	2026-08-25 20:09:50 +02:00
leonarski_fandClaude Opus 5	8d32024dd1	Ship jfjoch_viewer and rugnux as two packages, and cross-build rugnux for arm64 ... The viewer tarball also carried rugnux, jfjoch_extract_hkl and jfjoch_recompress. A GUI download that contains a batch processor is confusing on its own, and it forced anyone who only wanted rugnux to take Qt with it. JFJOCH_RUGNUX_ONLY is the viewer-only subtree minus viewer/ and tools/, so it needs no Qt at all, and each of the two options now yields one artifact holding one program: JFJOCH_VIEWER_ONLY jfjoch_viewer .tar.gz / installer / .dmg JFJOCH_RUGNUX_ONLY rugnux .tar.gz / .zip The two CLI tools are still built and no longer installed anywhere. rugnux gets a CPack component of its own, so its notices land in share/doc/jfjoch_rugnux. What makes the split possible is linking cuFFT statically in both products. It was the only CUDA component still dynamic - cudart and the fast-feedback indexer were already static - and shipping it as a .so meant each self-contained archive had to carry the library beside its executables and find it again through an $ORIGIN rpath. That rpath was set on jfjoch_viewer alone, while the same tarball installed three more executables, so those shipped with no runpath at all (cmake strips the build-tree one, which points at the build host's CUDA directory) and could not load the libcufft lying next to them. Static, an artifact is one file that runs: the x86_64 rugnux tarball needs only libc, libstdc++, libgcc_s, libm, libpthread, librt and libdl. The bundling code and the rpath both go away. libcufft_static.a carries a relocatable-device-code object, so a consuming executable needs a CUDA device link; CUDA 13 no longer ships the libcufft_static_nocallback.a that used to avoid this. CUDA_RESOLVE_DEVICE_SYMBOLS emits that step while leaving the host link driver alone, so the -march and -flto flags CI passes still apply. The server build keeps the shared library: its .deb/.rpm take CUDA from the distro, and every executable there would otherwise need the same device link. The guards that exclude server-side targets keyed on NOT JFJOCH_VIEWER_ONLY, which a rugnux-only build does not satisfy - it failed on jfjoch_writer pulling in JFJochImagePuller. They now key on JFJOCH_PORTABLE_ONLY, true for either product, rather than on one product's option in five places. docker/ubuntu2404 additionally cross-compiles rugnux for arm64 SBSA, which is both DGX Spark (GB10, sm_121) and Grace Hopper (GH200, sm_90); one binary with both fatbins runs on either. It needed three things beyond a cross gcc. arm64 is published on ports.ubuntu.com and Noble's deb822 sources carry no Architectures: field, so adding the architecture without splitting the entries 404s on every index. The CUDA cross packages are in neither the x86_64 repo nor the sbsa one but in cross-linux-sbsa, whose fatbinary_section.h ships only in the x86_64 target tree even though it is architecture-neutral. And HDF5 has two try_run probes, so qemu-user-static is needed as CMAKE_CROSSCOMPILING_EMULATOR; every other fetched dependency either guards its run-checks or has none. The cross-built tarball is one ELF aarch64 binary carrying all 17 GPU modules for both sm_90 and sm_121, needing no cuFFT and no CUDA runtime at run time. It is untested on hardware: XDS is x86-64 only, so CI can show it links but only a Spark or a GH200 can show it works. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SQjneRUssfhi1k9rq8Ts3h	2026-08-25 19:23:59 +02:00
leonarski_fandClaude Opus 5	46ed703eca	libjpeg-turbo: follow the parent build's toolchain when cross-compiling ... libjpeg-turbo is brought in with ExternalProject_Add rather than FetchContent, because upstream does not support inclusion via add_subdirectory. An ExternalProject is a separate cmake invocation that inherits nothing from its parent, and the CMAKE_CACHE_ARGS here named only the feature options, so it always configured for the build host. That is invisible in a native build and fatal in a cross build: the library compiles for x86_64 inside an aarch64 build and the mistake only surfaces at the final link of whatever consumes it, as an architecture mismatch on libjpeg.a rather than anything pointing at this file. rugnux reaches it through JFJochWriter -> JFJochPreview, so it is on the path of every build, not just the viewer's. Forward the toolchain file and the compiler. CMAKE_TOOLCHAIN_FILE is empty in a native build and cmake ignores it there, so nothing changes off the cross path. libjpeg-turbo selects its own SIMD from the target architecture, so this also gets the NEON kernels for free on aarch64 and stops nasm from being consulted at all; a cross-compiled libjpeg.a comes out ELF aarch64 with 14 NEON objects. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SQjneRUssfhi1k9rq8Ts3h	2026-08-25 19:20:43 +02:00
leonarski_fandClaude Opus 5	3ea1206775	Space-group search: raise the twin-law H bound from 1.70 to 1.85 ... Re-measured over ~780 reports - three batteries and four de-novo integration-radius arms - H is the only Stage-A guard that ever fires: 14 refusals on three crystals, and not one chi-squared-ratio refusal or b veto anywhere. Two of the three are the genuine trigonal twins, reading 1.90 and 1.91 on every arm and 3.61-4.80. The third is a weak tetragonal crystal reading 1.73-1.80 that is not twinned: its 422 is confirmed by every operator correlation, and three independent tests agree - our own L test on the P2(1)2(1)2(1) merge it was demoted into, xtriage on that same merge ("no twinning is suspected... most likely due to an NCS axis parallel to the twin axis"), and the arithmetic that a twin at the implied fraction caps twin-pair correlation at 0.55 while the four added operators score 0.84-0.90. Its excess is the coverage limit the comment above the bound already names: the added 422 operators exchange h and k, so they carry a systematic floor the parent's sign-flipping 2-folds do not. The two populations therefore collide at 1.80 and 1.90, not at 1.70, and the bound now sits at the midpoint of that window. Degrading the data - 4x sigma inflation, or an eighth of the sweep - drives the ratio towards 1 and never up, and the estimator is precise (bootstrap standard error 0.2-3.7% of the ratio), so the collision is a genuine population overlap rather than sampling noise. That also rules out scaling the bound by its own error, which at any useful multiple refuses half the battery. Inert on the shipped defaults: no crystal in the battery reads between 1.70 and 1.85 there. It changes one assignment on an experimental integration radius, from wrong to right. The committed twin test is unaffected - genuine promotions in that harness read 0.959-1.016 against 4.23-5.36 for its twin, so nothing lies in the interval that moved. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 19:17:16 +02:00
leonarski_fandClaude Opus 5	80e10f51b3	rugnux: measure and report diffraction anisotropy ... rugnux now says whether a dataset's fall-off is direction-dependent, and by how much. It corrects nothing and truncates nothing: no intensity is changed, no reflection is dropped on a directional criterion, and the written files do not depend on direction at all. Two quantities, because they are not the same thing. The anisotropic deltaB is the range of the principal components of the anisotropy tensor - a rate of fall-off. The diffraction limit along each principal direction is where <I/sigma(I)> in a 20 degree cone falls through 2 - where signal actually runs out. One battery case has only 0.28 A between its directional limits and a 58x ratio in cone <I/sigma>, so reporting either alone would miss it. The tensor is a Laue-constrained deviatoric ADP tensor fitted on INTENSITIES with no positivity cut, by weighted Gauss-Newton over 12 shells x 60 directions with a free constant per shell. Fitting amplitudes after a positivity cut, which is what xtriage and ctruncate do, destroys about 40% of the measured anisotropy - the cut keeps only the positive noise excursions in whichever direction has died, and that is the direction carrying the signal. Against the same 38 merged files rugnux reads 1.24x xtriage's eigenvalue spread and 1.61x ctruncate's; on strong near-isotropic data all three agree to a few percent, and they diverge exactly where a direction has died. The verdict is gated three ways - not detected, detected, or cannot determine - against the dataset's own systematic floor, measured in the tensor directions its Laue symmetry forbids. The floor cannot be measured on merged reflections, which have exact Laue symmetry by construction, so the floor is taken from the unmerged observations and the verdict is "cannot determine" without them. Triclinic has no forbidden subspace and always returns cannot determine. A cubic crystal returns exactly zero, because that is its symmetry and not a measurement. A second axis reports the resolution signature: a genuine Debye-Waller fall-off is linear through the origin in s^2, and a deficit that is flat is something else. Magnitude alone had promoted a crystal that is 68% not a Debye-Waller B into the top five of this battery; it now reads not detected with the caution attached. Following Sheriff & Hendrickson (1987) Acta Cryst. A43, 118-121 for the tensor and Popov & Bourenkov (2003) Acta Cryst. D59, 1145-1153 for the estimator. The directional limits are written as jfjoch_ local mmCIF items rather than _reflns.pdbx_aniso_diffraction_limit_*, whose dictionary definition is explicitly the ellipsoid fitted to a diffraction cut-off surface - a construction rugnux does not perform. The generic anisotropic B tensor items are written. Changes no existing number; only REPORT_VERSION moves, 1 to 2. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 19:13:16 +02:00
leonarski_fandClaude Opus 5	0f5a6e41d6	rugnux: report the Wilson B in --mode scale, and correct what the docs claim about the fixed integration radius ... --mode scale called AnalyzeTwinning but not CalcGlobalWilsonB, so WILSON_B= read nan there. Mirrors what --mode mx does; on one crystal scale mode now reports 72.03 against mx mode's 71.91 on the same data, and where the fitted B is not positive it still reads nan, which is the same verdict --mode mx reaches. The merged .mtz and .hkl are byte-identical before and after. docs/CPU_DATA_ANALYSIS.md and BraggStencil.h both said the flux the fixed r1 disk does not capture "is a function of resolution alone, which the per-shell scale absorbs". Neither half is true. The loss carries a directional component of several A^2 on top of the isotropic part. There is no per-shell scale, and there cannot usefully be one: every scale is fitted against a reference built from a reflection's own symmetry equivalents, equivalents share s^2 exactly, so any function of s^2 lies in the exact null space of the scaling model. What actually absorbs the isotropic part is the Wilson B, which is degenerate with it - so WILSON_B and _reflns.B_iso_Wilson_estimate carry an r1-dependent bias, measured at 18 A^2 of spread across four radius triplets on one crystal. The text also corrected a third error: in the default gaussian mode r1 is not the integration domain at all - the intensity is a profile-fit amplitude over a grid set by r2 - and a note now sits at the section a reader looking up the Wilson B actually lands on. Comments and documentation only for that part; verified by rebuilding and confirming byte-identical output with no flags. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 18:51:06 +02:00