172 Commits

Include renames

Author	SHA1	Message	Date
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	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	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_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	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	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	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	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
leonarski_fandClaude Opus 5	8db8267ff8	PCIe driver: build DKMS modules for the target kernel, not the running one ... dkms.conf quoted the make binary: MAKE="'make' -C src/ all". dkms passes the kernel it is building for by rewriting the leading "make" of that string into "make -jN KERNELRELEASE=$kernelver" (dkms 3.2.1, line 1446) - an anchored prefix substitution that the quotes defeat, so nothing was ever injected. The Makefile then hardcoded /lib/modules/$(shell uname -r)/build and would have ignored it in any case. With AUTOINSTALL=yes the module was therefore always compiled against the running kernel and installed into the tree of whichever kernel dkms was building for. A dnf update that pulls in a new kernel builds against the old one and drops the result in the new kernel's /extra, where it fails to load on the next boot. Crossing RHEL 9.4 to 9.5 it would also compile the wrong side of the vm_flags guard, which is how this was noticed. The Makefile now takes KDIR, defaulting to the running kernel exactly as before, and dkms.conf passes ${kernel_source_dir} - which dkms resolves for the target kernel before sourcing the conf, and which honours --kernelsourcedir. Dropping the quotes also lets dkms's -jN through, so the recursive invocations become $(MAKE) to keep the jobserver. Verified by building against a kernel other than the running one: the module now comes out carrying the target kernel's vermagic. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PLMZgfMEdtPBZt1F2rNbRA	2026-08-25 17:40:52 +02:00
leonarski_fandClaude Opus 5	59ebe8d9ae	PCIe driver: guard vm_flags_set for RHEL, which backported it into 5.14 ... RHEL and its derivatives report LINUX_VERSION_CODE 5.14.0 for the whole of el9 while backporting newer kernel APIs into it, so the version check alone picked the pre-6.3 branch on every el9 >= 9.5 and the module failed to build with "assignment of read-only member 'vm_flags'". HAVE_VM_FLAGS_SET could override it, but nothing sets it and dkms.conf does not pass it, so a build from the RPM had no way to reach it. vm_flags_set() and the const vm_flags member appear between kernel-5.14.0-440 and -450.el9, during the 9.5 development stream. RHEL_MINOR tracks the released minor exactly, so RHEL_RELEASE_CODE >= RHEL_RELEASE_VERSION(9,5) is the test: 9.0-9.4 (GA -427) do not have them, 9.5 (-503), 9.6 (-570), 9.7 (-611) and 9.8 (-655) do. el10 is 6.12-based and LINUX_VERSION_CODE already covers it, as it does the removal of no_llseek that the other guard in this driver handles. Spelled through a JFJOCH_RHEL_GE() helper rather than inline, because the obvious form #if defined(RHEL_RELEASE_CODE) && RHEL_RELEASE_CODE >= RHEL_RELEASE_VERSION(9,5) is a hard error on both gcc and clang for every non-RHEL kernel: && does not short-circuit past a parse error, and the undefined function-like macro leaves "0 (9,5)" behind. Also corrects > to >= on the upstream check. The wrappers landed in 6.3, so a vanilla 6.3.0 kernel was taking the pre-6.3 branch. Generated code on el8 is unchanged. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PLMZgfMEdtPBZt1F2rNbRA	2026-08-25 17:40:44 +02:00
leonarski_fandClaude Opus 5	ef07770c5f	rugnux: name the unmerged export from the prefix, and drop centring absences ... --export-unmerged and --export-unmerged-partials no longer take a filename; they write <prefix>_unmerged.mtz and <prefix>_unmerged_partials.mtz, as --write-process-h5 already does for <prefix>_process.h5. Lattice-centring absences are no longer written. They are integrated on purpose - prediction runs in P so the space-group search can confirm or disprove the centring - but in an exported file they cost the reader the answer: pointless reads the interstitial nodes, takes the lattice for primitive, and demotes I23 to P2_1 3, while aimless roughly halves its <I/sigma> merging them. They were also only present when the indexer had settled on the conventional centred cell, so the file's content depended on which of two equivalent cells it picked. Screw and glide absences are still written. They are the evidence a space group is chosen on, so a program reading this file can check that choice independently; deleting them turns pointless's test into an assumption ("we cannot determine if the reflections are truly systematically absent"). Deleting them changes no merging statistic. XDS and DIALS draw the line in the same place - XDS ships screw absences and never measures a centring one, and DIALS's absence machinery has only screw-axis classes. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 17:21:21 +02:00
leonarski_fandClaude Opus 5	bb5aaca68e	rugnux: sum each rotation reflection's partials into one full on export ... --export-unmerged now writes one row per reflection with its partials summed, which is how a rotation dataset is normally handed to a scaling program. The previous behaviour is still available as --export-unmerged-partials. Partials made the file's usefulness depend on the reading program's partial-assembly settings. On an orthorhombic case only 31% of partial sets passed aimless's default PARTIALS test, so it merged 2% of the file: multiplicity 4.7 against our own 12.4, CC1/2 0.788, and CC against our merged intensities 0.806. Summed, aimless uses 89% of the file and rejects nothing: multiplicity 12.5, CC1/2 0.931, completeness 96.1 to 98.0, pointless Laue confidence 0.669 to 0.792, CC 0.848. The other two test crystals are ties overall and win their outer shells, and the anomalous signal comes out stronger from the fulls. iotbx.merging_statistics, which never assembled partials at all, now reports real merging statistics rather than statistics of parts. Events are grouped by Combine()'s own rule so the file and the merge assemble exactly the same reflections; the sum is plain with variances in quadrature and no partiality division, which reproduces the merge's full times FRACTIONCALC to a few percent. Per-part metadata is combined on a partiality-weighted centroid rather than an intensity-weighted one: 8-41% of events have parts summing to zero or less, where intensity weights are undefined or sign-flipped, and 10-21% of intensity-weighted centroids fall outside the event's own frame range. Events below --min-partiality are not written. Declaring a reflection whose rocking curve caught a thousandth of itself as a complete measurement gives a scaling program noise with a small sigma and it weights it heavily; there is no partial test to catch it once it is a full. This is the same constant already applied to the same quantity in the merge, and it is what takes the orthorhombic case from CC 0.219 to 0.848. --min-partiality 0 writes every event. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 16:18:14 +02:00
leonarski_fandClaude Opus 5	5248b1bc00	rugnux: export the integrated observations as an unmerged MTZ ... Adds --export-unmerged <file.mtz>, in --mode mx and --mode scale alike. rugnux could only write merged reflections, which closed it off from the programs that consume unmerged observations - aimless, pointless, careless and iotbx.merging_statistics all read this file. The column layout follows what pointless itself writes (H K L M/ISYM BATCH I SIGI FRACTIONCALC XDET YDET ROT LP FLAG), with DELPHI, ZETA, BGMEAN and BGVAR added because we have them and a scale model can use them. Three details decide whether the file is usable: Lorentz-polarization is applied and recorded in LP. It is per-observation geometry spanning a factor of ~120 across a sweep and no reading program can recover it; merging with no scale model at all gives R_meas 0.372 / 0.346 / 0.324 in the low shells without it against 0.183 / 0.218 / 0.257 with it. The partiality is not divided out - it stays in FRACTIONCALC - and neither is the per-image scale, since these programs fit their own. The observations are partials and are flagged as such, packed as 256*M + ISYM with LDTYPE=1. Without the flag pointless reads every part as a whole observation and mis-assigns the symmetry; with it, a tetragonal case assembles 8.29M parts into 1.15M observations and comes back as its own space group at confidence 0.92. The scan axis is written as the negation of the stored goniometer axis, which is the Cambridge convention: against pointless's own orientation matrix that agrees to 0.6 degrees, where the axis as stored disagrees by 40. Merging the exported file with aimless reproduces rugnux's own merge to CC 0.9997 on a tetragonal case and 0.9978 on a cubic one, and the anomalous signal survives. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 15:21:57 +02:00
leonarski_f	61c603b274	v1.0.0-rc.163 (#73) ... * Packaging: each package installs its license notices under a directory of its own - `share/doc/jfjoch_broker`, `share/doc/jfjoch_writer`, `share/doc/jfjoch_viewer`, `share/doc/jfjoch_driver_dkms` - instead of all of them into the shared `share/doc/jfjoch`, so `jfjoch` and `jfjoch-writer` can be upgraded one at a time instead of only together. Reviewed-on: #73 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-08-25 13:38:29 +02:00
leonarski_fandjungfrau	4dc2534dbf	v1.0.0.rc-162 (#72) ... **Files written by Jungfraujoch now import correctly in DIALS, XDS and pyFAI.** A tilted detector, a grid scan, a still recorded at a goniometer position, and saturated or unreadable pixels were each described in a way that a third-party program acted on wrongly. If you process Jungfraujoch data outside Jungfraujoch, prefer this release to any earlier one. * HDF5: the detector tilt (`rot1`/`rot2`/`rot3`) is exported correctly in the NXmx transformation chain; untilted geometries are unaffected. * HDF5: a still recorded at a goniometer position is no longer read back as a single image, and a grid scan records a stationary spindle so a program that requires a rotation axis can open it. * HDF5: the sample transformation chain is written in mounting order, with a Smargon head position told apart from the spindle, one entry per image, `module_offset` as a float unit vector, and `offset_units` on every offset. * HDF5: saturated, underloaded and unreadable pixels are described so a downstream program masks them - `saturation_value`, `underload_value`, `error_value` and `bit_depth_readout` are written correctly, and a data file missing next to a VDS master reads as the error marker rather than as zero counts. * HDF5: the rotation axis is read back under whatever name it carries, and `mirror_y` records whether the assembled image is mirrored in Y relative to the detector's raw readout. * A grid scan and a goniometer axis can both be set; they are no longer alternatives. * `images_per_file` is chosen from the acquisition when it is not given: a rotation sweep of at most 20000 images goes into a single data file, a grid scan splits on whole fast-axis rows, and stills and serial keep 1000. * The writer refuses a stream whose start message declares a different pixel format than its images carry, and a DECTRIS detector sending signed images is no longer declared unsigned. * The image stream can carry the sample transformation chain (`transformations`, in the END message); a producer that does not send it gets the same chain built by the writer. * rugnux: fixing the space group with `-S` no longer prevents the lattice from being found - a lattice indexed in a different setting is reindexed into that group's own setting, and a run whose crystal does not have that group's lattice stops and names the cell it indexed as, rather than reporting statistics that cannot describe it. * rugnux: the per-image resolution estimate now predicts the resolution the merged data reach rather than the highest-resolution spot found, and is reported as `SPOT_RESOLUTION_ESTIMATE`. * rugnux: two runs of the same command on the same images produce the same merged intensities; the azimuthal profile written alongside them is not yet reproducible in the same way. * rugnux: the offline lattice refinement is bounded by iterations rather than by a wall clock, so a loaded machine can no longer refine to a different lattice; a live acquisition keeps its real-time bound. * rugnux: the detector-frame modulation correction is fitted on a grid spanning the detector, so whether it is applied no longer depends on how far integration reached. * rugnux: the geometry pre-pass no longer writes `<prefix>_01.mtz`, `_01.cif`, `_01.hkl` and `_01_image.dat`; the refined second pass writes those files under `<prefix>`, and that is the result to use. * rugnux: `_process.h5` describes the pixel format of the images it links to, and is written on a thread of its own. * rugnux: the detector geometry is also logged in XDS's convention (`ORGX`/`ORGY`, detector axis vectors, rotation axis), so it can be compared with an XDS refinement. * rugnux: an image integrated in pyFAI through the `.poni` file written by `--mode calibration` comes out with the correct azimuth, and the file declares pyFAI's `orientation`, which needs pyFAI 2024.01 or newer. Radial integration is unchanged. * rugnux: a rotation run is substantially faster throughout - beam-stop detection, first-pass indexing, geometry refinement, integration, scaling and merging - and observations outside the scaling resolution range are dropped as they are ingested. The refined geometry, the space group chosen and the merged statistics are unchanged. * Faster spot finding and indexing, on the broker as well as in rugnux; the spots found and the lattices indexed are unchanged. * A run reserves substantially less GPU memory: nothing is allocated for buffers that are never read, and a worker builds only the engines it uses. * rugnux: with `-N` left at its default the per-image loop of `--mode mx` uses at most 16 workers per GPU, rather than one per hardware thread; an explicit `-N` is obeyed as given. * CUDA 12 builds now contain device code for Volta, so the RHEL 8 packages and the portable Linux `.tgz` run on a V100; the CUDA 13 artefacts (RHEL 9, Ubuntu, Windows) remain Turing and newer. * The build resolves a single Eigen for the whole project, and refuses to configure if Ceres picks up a different one; a build that mixed two Eigen versions was undefined behaviour and crashed at -O2. * Documentation: a security page, and the supported GPU generations and minimum NVIDIA driver version of every released artefact. **Breaking change to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.162, `frontend/src/client`): * `dataset_settings.images_per_file` is no longer `default: 1000` and no longer accepts `0`; it is optional, and its minimum is 1. A client sending `0` (previously "one file for the whole run") is now rejected - omit the field instead, which for a rotation sweep gives the same single file. * `file_writer_format` now defaults to `NXmxVDS`, matching the server's own default and the layout recommended for DIALS, XDS and CrystFEL. A generated client that fills in schema defaults and does not set the format explicitly will write VDS masters where it previously wrote legacy ones; set `NXmxLegacy` explicitly to keep them. --------- Co-authored-by: jungfrau <jungfrau@mx-aare-test.psi.ch> Reviewed-on: #72 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-08-25 08:21:39 +02:00
leonarski_f	538f3504d3	v1.0.0.rc-161 (#71) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * **rugnux: significantly better quality of results, and faster.** A large rework of integration, scaling, merging, geometry refinement and space-group determination, together with measurements the program previously made no attempt at - the direct beam before indexing, the beam stop, the goniometer rotation scale, and the stretches of a sweep the crystal did not deliver. A rotation dataset typically gains observations at better <I/sigma> and R_meas, and every `mx` and `scale` run writes a `<prefix>_report.txt` results report modelled on XDS's `CORRECT.LP`. Many defaults moved with it: spot detection is self-calibrating, beam-stop detection and rotation geometry post-refinement are on, resolution limits default to as far as the detector reaches, and ice-ring handling engages only where the crystal is measured to have ice. * **jfjoch_viewer:** the beam-stop shadow, the detector calibration and the beam-centre measurement are reachable from "Analyze dataset"; the settings panel reports how the sample moved and how polarized the beam was; image rendering and interaction are faster. * **Performance:** bitshuffle+LZ4 images are decoded on the GPU rather than on the host, with the bitshuffle inverse fused into preprocessing so the decompressed frame is never held in device memory. * **Broker, writer, packaging and build:** image-slot lifetime and locking fixes, per-image datasets sized by the images actually written, the Debian/Ubuntu broker package renamed to `jfjoch`, and `image_analysis` compiling under MSVC again. **Breaking change to the rugnux command line:** * `--azint-only` and `--scale` are **removed**, replaced by `--mode azint` and `--mode scale`; the full pipeline is `--mode mx` and remains the default. A script passing the old flags now fails with the list of valid modes rather than silently running the wrong one. * `-t`/`--stride` is **refused on rotation data**: skipping frames cuts every reflection's rocking curve, so the combined fulls and their partiality would be measured over frames the sweep never recorded. Select a contiguous range with `-s`/`-e` instead. `--mode azint` and `--force-still` still take a stride. **Breaking changes to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.161, `frontend/src/client`) or read the affected fields as optional: * `image_scale_b` is removed from the `plot_type` enum, so a client requesting that plot now gets an error rather than a curve. * `azim_int_settings.high_q_recipA`, `spot_finding_settings.high_resolution_limit` and `spot_finding_settings.low_resolution_limit` are no longer `required`. All three mean "no limit at that end" when unset and are omitted from the response instead of carrying a placeholder value, which raises in a client generated from an rc.160-or-earlier spec. A value of 0 is still accepted and means the same thing. **Breaking changes to the stored formats** - a consumer reading these fields must treat them as optional: * The per-image image-scale B factor is no longer computed, so `/entry/MX/imageScaleBFactor` is absent from newly written HDF5 files and the corresponding key is absent from the CBOR DataMessage and END blocks. Files written by rc.160 and earlier still contain it and still open; nothing in the pipeline reads it any more. * `_reflns.jfjoch_diffrn_ISa` now carries the whole-range `1/sqrt(a*b)` that XDS's ISa denotes, and the error-model `a` and `b` are reported in XDS's convention; the strong-reflection asymptote moves to `_reflns.jfjoch_diffrn_ISa_asymptotic`. **A file written by an earlier version carries the asymptote under the plain `ISa` name.** Reviewed-on: #71 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-08-13 17:03:10 +02:00
leonarski_f	67dca388bd	v1.0.0-rc.160 (#70) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #70 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-19 09:39:28 +02:00
leonarski_f	dd0bffb283	v1.0.0-rc.159 (#69) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #69 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-13 13:54:03 +02:00
leonarski_f	451310f43d	v1.0.0-rc.158 (#68) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * Analysis: The azimuthal-integration solid-angle correction now follows the incidence angle to the detector normal (`cos^3` of that angle) instead of `cos^3(2*theta)`, so it is correct for a tilted detector and matches PyFAI `solidAngleArray` and MAX IV azint (unchanged for an untilted detector). Crystal geometry refinement (`XtalOptimizer`) no longer silently ignores an imported PONI `rot3` (rotation about the beam): it is applied as a fixed rotation in the residual so refinement stays consistent with the rest of the pipeline. Polarization and azimuthal binning already honoured `rot3` through the full PONI rotation. * jfjoch_viewer: Open datasets on the WSL2/UNC filesystem (paths starting `\\`); write processing outputs next to the input file, with a Browse button and independent `_process.h5` / merged `.mtz`/`.cif` toggles; and show the determined space group in the merge-statistics window. * rugnux: Accept an absolute `-o` output prefix in offline processing. * Packaging: The self-contained Linux viewer `.tgz` now bundles cuFFT, so it runs without a system CUDA toolkit (`.deb`/`.rpm` are unchanged, distro-managed). * Docs: Bring the analysis references up to date with the code. `docs/CPU_DATA_ANALYSIS.md` now reflects the unified profile-fit Bragg integration engine, multi-lattice indexing, azimuthal phi binning, the radial parallax/bandwidth profile with sub-pixel centring, the rot3d capture-fraction handling and the automatic CC1/2 resolution cutoff, and drops the descriptions of features that were never implemented (French-Wilson amplitudes, the still excitation-error partiality model); `docs/RUGNUX.md` documents the new `--resolution-cutoff`/`--resolution-cc-target`/`--resolution-shells`, `--min-captured-fraction`, `--mosaicity`, `--reference-column`, the azimuthal correction toggles and the geometry-override options, and corrects the `-N` default. The outdated in-source design notes (ICE_RING_DETECTION, BRAGG_INTEGRATION_ENGINE, NEXTGEN_INTEGRATOR) are removed.Reviewed-on: #68 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-12 19:42:29 +02:00
leonarski_f	54c0100e8e	v1.0.0-rc.157 (#67) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * rugnux: Rebrand the offline data-processing subsystem as `rugnux` and consolidate all offline analysis into the single `rugnux` binary - `jfjoch_process` is now `rugnux`, the former `jfjoch_azint` is now `rugnux --azint-only`, and `jfjoch_scale` is now `rugnux --scale` (see the new docs/NAMING.md and docs/RUGNUX.md). Scaling and merging are on by default for rotation and stills (`--no-merge` disables them), replacing the previous opt-in `-M, --scale-merge`. * rugnux: CLI fixes - default `-N` to all hardware threads, parse numeric option arguments strictly (reject non-numeric or trailing input instead of silently yielding 0), require `--wavelength > 0`, and correct the reproduced command line and `--scale` reference-cell handling. * rugnux: De-novo space-group improvements - recover genuine high symmetry and centred Bravais lattices from intensities, add an automatic CC1/2 high-resolution cutoff, and report L-test twinning statistics. * rugnux: Index weakly-diffracting low-resolution rotation data that previously failed (e.g. F-cubic crystals that diffract only to ~4 A on a detector reaching ~1.5 A). The per-frame indexing gate now measures the indexed fraction only within the resolution range the lattice actually diffracts to, so the many sub-diffraction ice/noise spots no longer make the fraction floor unreachable; the two-pass first pass tries several image-sampling schemes (spread across the whole rotation vs a consecutive wedge whose native stride keeps a reflection's rocking curve continuous, letting the FFT resolve a long axis) and keeps the one that indexes the most frames; and the de-novo space-group search no longer discards all reflections (and crashes) when every resolution shell falls below <I/sigma> = 1. * rugnux: Lower the low-resolution R-meas for strongly-diffracting rotation data - drop edge-of-sweep truncated fulls whose rocking curve was captured below `--min-captured-fraction` (default 0.7 for rotation), and report R-meas only over the observations kept by outlier rejection (matching XDS). The 0.7 default also strips the partiality-extrapolated fulls that dominate the intensity second moment on weakly-diffracting crystals, so the de-novo space-group search is no longer starved by the error-model I/sigma floor and recovers the correct symmetry (e.g. the F-cubic Benas crystals: Benas_3 -> F432, Benas_7 -> P6122, instead of P4/P1); on the reference battery every other crystal keeps its space group. * rugnux: Write the refined geometry (beam, tilt, axis) to _process.h5 and place non-standard mmCIF items under a reserved `jfjoch` prefix. * jfjoch_broker: Ordinary acquisition failures (receiver/writer/analysis problems, missed packets, writer disconnect) now return to the Idle state with an Error-severity message, so a run can be retried without an expensive re-initialisation; only failures that leave the detector in an undefined state (new JFJochCriticalException, e.g. PCIe/FPGA faults) go to the Error state and force re-initialisation. * jfjoch_broker: A synchronous /start now reports its failure to the HTTP caller instead of returning HTTP 200, and an incomplete or truncated dataset (missing packets, writer disconnect) is reported as an error rather than a "reduce frame rate" warning. * jfjoch_broker: Drop uncollected placeholder rows (number = -1) from the scan_result REST endpoint. * jfjoch_broker: Fix the inverted per-image compression ratio reported by the Lite receiver (was compressed/uncompressed instead of uncompressed/compressed). * jfjoch_broker: Bragg integration adds a quantization-noise variance floor with a box-sum fallback, and treats the type-maximum marker as an invalid pixel for unsigned image types. * jfjoch_writer: Detect file-overwrite conflicts at start for back-channel transports, and reset the writer when end-of-collection finalisation fails. * jfjoch_viewer: Preview overlays follow the geometry (resolution/ROI arcs, true beam centre, predictions, coral secondary-lattice spots, legend), add save-as-JPEG, and fix an HTTP live-follow memory leak. * Frontend: Improved aesthetics and usability, and added in-browser pixel-mask and JUNGFRAU-pedestal visualisation. * CI: Name the Windows installer jfjoch-viewer-* instead of jfjoch-*.Reviewed-on: #67 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-11 07:19:11 +02:00
leonarski_f	d6389e12da	v1.0.0-rc.156 (#66) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * jfjoch_process: Major rotation (rot3d) data processing overhaul - robust profile-fit integration, Cauchy-loss scaling with optional absorption surface, de-novo indexing and space-group/centering determination fixes, and merging statistics + ISa in the mmCIF output. * jfjoch_process: Add EXPERIMENTAL ice-ring detection (--detect-ice-rings) that excludes ice reflections from scaling. * Compression: Add BSHUF_ZSTD_RLE_HUFF, make compression size-aware (drop frames that don't fit rather than aborting), and add the jfjoch_recompress tool. * jfjoch_viewer: Report "Multiple lattices detected" and grey out "Analyze dataset" on a live connection. * jfjoch_broker: Write smargon chi/phi goniometer positions to NXmx; read sensor thickness/material from HDF5 metadata. * CI: Build Windows (CUDA and non-CUDA) installers.Reviewed-on: #66 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-03 19:18:56 +02:00
leonarski_f	54c667190f	v1.0.0-rc.155 (#65) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * jfjoch_process: Remove pixelrefine option (replaced with ProfileIntegrate2D) * jfjoch_viewer: Some graphical improvements. * jfjoch_viewer: Simplify und unify data analysis settings. * jfjoch_writer: Add TCP keepalive to increase robustness if jfjoch_broker "dies" in the middle of data acquisition. Reviewed-on: #65	2026-06-25 22:01:48 +02:00
leonarski_f	6136f858af	v1.0.0-rc.154 (#64) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * jfjoch_broker: Fix to TCP file pusher (remove kernel zero copy to improve reliability) Reviewed-on: #64 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-06-25 18:12:00 +02:00
leonarski_f	75e401f0e5	v1.0.0-rc.153 (#63) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * jfjoch_broker: Add EXPERIMENTAL pixelrefine mode for image processing * jfjoch_broker: Allow to load user mask from 8-bit and 16-bit TIFF files * jfjoch_broker: Add ROI calculation in non-FPGA workflow * jfjoch_broker: Fixes to TCP image pusher * jfjoch_broker: Remove NUMA bindings * jfjoch_broker: Improvements to indexing * jfjoch_broker: For PSI EIGER, trimming energies are taken from the detector configuration (now compulsory) instead of hardcoded values * jfjoch_writer: Save ROI definitions and the per-pixel ROI bitmap in the master file; azimuthal ROIs support phi (angular) sectors * jfjoch_viewer: Major redesign with dockable panels and saved layouts, plus on-canvas creation/move/resize of box, circle and azimuthal ROIs * jfjoch_viewer: Run jfjoch_process reprocessing jobs from inside the GUI and overlay per-run results Reviewed-on: #63	2026-06-23 20:29:49 +02:00
leonarski_f	c49bd2ac3b	v1.0.0-rc.152 (#62) ... * jfjoch_broker: Fix bounds for azimuthal integration for Q spacing (allow Q of 1e-5) * jfjoch_viewer: Adjust Q bounds for azimuthal integration * jfjoch_azint: Add tool to do quick azimuthal integration Reviewed-on: #62	2026-06-17 20:36:24 +02:00
leonarski_f	ef52dac2ee	v1.0.0-rc.151 (#61) ... * jfjoch_broker: For PSI EIGER detector allow to disable individual half-modules by putting empty hostname Reviewed-on: #61 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-06-16 14:13:29 +02:00
leonarski_f	90e804acd7	v1.0.0-rc.150 (#60) ... * jfjoch_broker: When in FPGA workflow (with PSI detectors) azimuthal integration might be forced to CPU - this will require more computational power, but it enables more integration bins and reports standard deviation of each bin. * jfjoch_broker: Raise error if one is in FPGA flow and there are too many azimuthal integration bins. Reviewed-on: #60	2026-06-15 20:24:15 +02:00
leonarski_f	ea575f790a	v1.0.0-rc.149 (#59) ... * XDS plugin: Fix HDF5 mutex to run on multiple processors Reviewed-on: #59	2026-06-13 21:27:41 +02:00
leonarski_f	cc3eb8352c	v1.0.0-rc.148 (#58) ... This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144. * jfjoch_broker: Improve azimuthal integration (add <I^2> calculation) * jfjoch_broker: Fixes around indexing, aiming to handle multi-lattice crystals (work in progress, it is not fully integrated) * jfjoch_writer: Save mean(I), stddev(I), and count(I) for each azimuthal bin Reviewed-on: #58	2026-06-08 08:30:35 +02:00
leonarski_f	75de40f52b	v1.0.0-rc.147 (#57) ... This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144. * jfjoch_viewer: Add reciprocal space viewer * jfjoch_process: Two pass algorithm that does spot finding/indexing + integration of full dataset * jfjoch_process: Improve logic for rotation indexer, to make execution more deterministic (still work in progress) Reviewed-on: #57 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-06-02 11:49:24 +02:00
leonarski_f	fc68a9baed	v1.0.0-rc.146 (#56) ... This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144. jfjoch_process: Generate a dedicated file (_process.h5), which can be used as a replacement for the _master.h5 file for a reanalyzed dataset. jfjoch_process: Improve the performance of scaling and merging, implement on the fly scaling. jfjoch_writer: All final data analysis results are repopulated in the _master.h5 file. jfjoch_scale: Dedicated tool for rescaling/merging existing data. jfjoch_viewer: Fix bugs where pixel labels where displayed on a wrong pixel. WARNING! Scaling and merging are experimental at the moment, and may not provide reasonable results for the time being. Reviewed-on: #56	2026-05-28 18:48:35 +02:00
leonarski_f	caef26873e	v1.0.0-rc.145 (#55) ... This is an UNSTABLE release. The release has significant modifications for HDF5 writing logic - in case of troubles go back to 1.0.0-rc.144. * **Default HDF5 writing mode is with VDS, not soft-links** - this improves DIALS compatibility and makes format more future-proof, NXmx legacy format might be phased-out in the future. * XDS plugin: Improve performance of VDS reading. * jfjoch_writer: Significant improvement on how file systems I/O are handled through a dedicated pass-through VFD. * jfjoch_writer: Clean-up of HDF5 routines to better handle issues. Reviewed-on: #55	2026-05-06 21:50:02 +02:00
leonarski_f	7d34e8a049	v1.0.0-rc.144 (#54) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Improve performance of preview JPEG image generator at receiver startup (saving about 150 ms on measurement start for 16M) Reviewed-on: #54 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-05-01 17:06:36 +02:00
leonarski_f	6e0bb971ac	v1.0.0-rc.143 (#53) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. jfjoch_broker: Avoid copying gain calibration together with DiffractionExperiment Reviewed-on: #53	2026-04-30 22:16:50 +02:00
leonarski_f	87fde1b32e	v1.0.0-rc.142 (#52) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * Support for newer CUDA architectures (notably Blackwell); minimum CUDA version 12.8 * Minor changes to jfjoch_process, jfjoch_fpga_test and jfjoch_lite_perf_test to make them more consistent Reviewed-on: #52 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-30 16:47:53 +02:00
leonarski_f	d760b12a18	v1.0.0-rc.141 (#51) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Azimuthal integration mapping is generated with parallel computations, significantly reducing setup times * frontend: Fix selection of FFTW in indexing settings Reviewed-on: #51 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-30 13:04:54 +02:00