179 Commits

Include renames

Author	SHA1	Message	Date
jungfrauandClaude Opus 5	5ee0f22a61	Build the detector's lookup tables once, not once per worker ... The image loop gives every worker its own analysis engine, so a run builds ninety-six of them. Each one derived, from scratch, tables that are the same in all of them: the byte-per-pixel mask, the resolution mask, the radial kernel, and the checksum that names the shared device tables. The checksum was the worst of it, because it is part of the cache KEY and so is computed before the lookup - a hit still hashed the whole table. On a 16 Mpx detector that is the bin table, the corrections and the mask, 126 MB an engine, about twelve gigabytes over a run, to answer a question whose answer had not changed. The header said it cost nothing measurable; a profile says otherwise, and says it is worst exactly during the ramp when the machine has nothing else to do. It cannot simply be remembered against the address, which is what it exists to catch: a buffer can be freed and another allocated where it was, and the cache would then hand back a device copy of something else. So the owner of the bytes computes it instead. The azimuthal mapping writes its two tables in its constructor and never again. The pixel mask re-derives its binary form and its checksum on every path that changes the mask, and all of those paths are now private to the class. The key therefore still describes the bytes as they are at the moment of the lookup. The resolution mask was two passes over every pixel - a float comparison into a vector<bool>, then a bit-by-bit repack - in each of the ninety-six. It is one pass now, writing the packed form directly, built once for the limits asked for and handed out as a shared pointer so a worker keeps the mask it was given. The radial kernel is cached on the six numbers it is derived from. Nothing computes a different value; only who computes it changes. Byte-identical merged output on a 16 Mpx set and on a small one. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011n8riB6X59oRjkrSHzNPAU	2026-08-23 12:59:58 -04:00
jungfrauandClaude Opus 5	27020d27e9	Take the merge's per-observation sweeps off one thread ... Of the seventeen seconds a high-multiplicity crystal spends in scaling and merging, only three are GPU work. The rest is the host, and most of it was running on one or two cores of forty-eight. Eight of those passes are elementwise maps over the observation array - restoring the scaling correction at the start of a pass, saving it before the pass filters, scattering it back from the device, the zeta filter, the frame rejection, the two gathers that hand it to the device again, and the collapsed-scale ratio. Each reads and writes an eighty-byte record per observation, each ran serially, and each runs once per cycle with five cycles in a run. They are independent per element, so chunking them changes nothing but the wall clock. The zeta filter's drop count is now one atomic add per chunk rather than per observation, and it is an integer, so no arrival order can move it. The download of the combined fulls did the same work twice over: `assign(nf, Obs{})` zeroed a quarter of a gigabyte that the next loop overwrote completely, fifteen scratch vectors were allocated and zeroed afresh every cycle, and the gather from them was a three-million-iteration serial loop. The scratch is now kept between cycles and the gather is chunked. The correction surfaces were the last of it. Their inner pass sums the reference intensity of every usable full, thirty-nine times a run, and a comment asked for per-worker accumulators if it ever mattered. It does now, but per-worker accumulators would re-associate the double sums. The fulls are already grouped by a stable counting sort, so walking that grouping visits each group's members in increasing index - the order the serial loop added them in - and the sums keep their exact sequence. Copying the four fields the pass actually reads into a packed record first is what makes it pay: what kept this serial was not the addition but the random read across 265 MB of fat structs, and 53 MB read in order is a different thing. Ingest is parallel over frames now, which is safe because a frame's mean background is still summed in that frame's own order by one thread - it is the incident-flux meter and it has to be exact. The larger rewrite it deserves, sorting a narrow key first and building the fat record only for the ten per cent that survive the resolution cut, is left alone. Measured with the surrounding commits: a high-multiplicity set 35.6 s -> 32.4 s, a large-cell one 52.6 s -> 46.1 s, byte-identical merged output on both. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011n8riB6X59oRjkrSHzNPAU	2026-08-23 12:59:35 -04:00
jungfrauandClaude Opus 5	0fed94d75b	Gather post-refinement's partials without touching four gigabytes twice ... Post-refinement fits eight numbers, and it selects the twenty thousand best-recorded events to fit them from. Before it can select, it copies every integrated partial into an array of its own and sorts it. On a large cell that is 63 million of them, and the phase took 8.5 s of a 56 s run. Almost none of that was the sort. `std::vector<Partial> pts(n)` value-initialises: one thread writes 3.5 GB of zeroes, page by page, before the parallel fill overwrites every byte of it - and being the first touch, it also decides where the pages live, so the whole array lands on one NUMA node and every later pass over it runs at one node's bandwidth. The same again for the sorted copy. Allocate the storage without initialising it and let the parallel fill be the first touch. The record itself carried more than the sort reads. `angle_rad` is a function of the image number that the goniometer can give back on demand, and the two observed positions are wanted only by the distance step, and only for the twenty thousand it keeps. Storing what is read - and as the floats the fields already were, since widening a float to a double is exact - takes the record from 56 bytes to 32, which is a third off the fill and half off the sort's element moves. Then three passes that walked the whole array to no purpose. The h range is now taken in the count pass, which reads the same reflections anyway; the bucket histogram in the fill pass, which already has h in hand. The event split walked serially and grew its output by doubling - about a gigabyte of pure copying - although h is the leading sort key, so a rocking event never crosses an h bucket: count per bucket, prefix, fill in parallel, and the events come out in the order the serial walk produced them. And the copy of the whole event list, made only so that nth_element could destroy the original, is now an index array. Every one of these is the same arithmetic in the same order. Measured on a large-cell rotation set, with the two commits that follow: 52.6 s -> 46.1 s, and the merged .hkl, .mtz and .cif are byte-identical. `part_less` is deliberately left as it was, not a total order: what makes it reproducible is that each bucket reaches the sort in gather order, and the new chunking is still a contiguous span of that order. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011n8riB6X59oRjkrSHzNPAU	2026-08-23 12:59:35 -04:00
jungfrauandClaude Opus 5	4a537dbfc2	Bin the error model's samples without sorting them ... The (a, b) fit wants sixteen equal-count bins in I^2 and takes three medians out of each. It was getting them by sorting the whole pool - millions of 32-byte samples - and it did that fourteen times a run: the fit runs once per merge and twice where the resolution cutoff refits, the outlier refit doubles it again, and there are five merges. Each call also took its pool BY VALUE, so every one of those began by copying tens of megabytes, and each bin then built three more vectors by push_back to hand to a median. A bin only has to be the right SET. Put each boundary in place with nth_element instead, splitting the boundaries down the middle so every level halves the range it works on - four levels of linear work against n log n - and take the three medians straight off the bin's own span with the field wanted, which is what median_of was doing anyway: it returns the lower median, exactly the element nth_element leaves at that index. No copy is made at all, and the sixteen bins are disjoint so they divide over the cores. The comparator is now total. The sort it replaces was not stable, so which of two samples of equal I^2 landed in which bin was decided by the order the pool happened to arrive in - and the refit is handed a different order from the first fit. Ordering on the remaining fields, which are in the same cache line, makes the bin a property of the samples instead. This is why the merged intensities are not byte-identical to the previous release on about half a percent of reflections, at a median difference of zero and a worst case of 1.2e-2: those are the ties, whose old resolution was arbitrary. Every fitted (a, b, ISa, chi2) in the run agrees to four significant figures. The per-group outlier median goes the same way. It was building a vector per ASU group to hold a handful of floats - over a million allocations, their growth and their frees, five times a run - where the counts were already to hand from the pass above. One flat array with a per-group span gives the identical median, since a median does not care how the multiset was laid out. Measured together with the previous commit on a high-multiplicity rotation set: 38.3 s -> 35.1 s. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011n8riB6X59oRjkrSHzNPAU	2026-08-23 11:52:54 -04:00
jungfrauandClaude Opus 5	c9fc46e6e2	Stop making the first pass write the files the second pass replaces ... Pass 1 exists to choose the space group and post-refine the geometry. Its merged intensities are discarded - pass 2 remakes them seconds later at the refined geometry, and that is the answer anyone reads. It was nonetheless writing the full set of merged files at the end of every pass 1: a mmCIF of every unique reflection (22 MB on an ordinary crystal, 48 MB on a crowded one), an .hkl, an .mtz and the per-image scaling table, all through one thread. Measured on an ordinary rotation set: 0.60 s of a 15 s run, and pass 2's identical block right after it takes another 0.585 s to write the files that are kept. The pass-2 quality guard is untouched, which is what disqualified an earlier attempt at this: has_merge_statistics is set at the merge, well above the write, so pass 1 still reports the completeness and CC1/2 the guard compares against. Nothing numeric moves - the same run measures 38.5 s before and 36.6 s after with a byte-identical .hkl. Also hoist the pixel-mask accessor out of the preprocessor's per-pixel loop. It called .at() on every pixel of the detector - 18 million bounds checks per engine, and an engine is built per worker per pass - for a bound the loop already respects, which stopped it vectorising. The <prefix>_01.mtz/.cif/.hkl are documented output, so this is a deliberate behaviour change: the pre-pass result is no longer written. If it is wanted for comparison it should come back behind a flag rather than by default. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011n8riB6X59oRjkrSHzNPAU	2026-08-23 11:52:37 -04:00
jungfrauandClaude Opus 5	16639e9de2	Add up the profile accumulators in an order the schedule cannot change ... Every accumulator in this file that could be an integer already is one, and the spot finder's reduce_rings_shared says why: a preprocessed pixel is an exact int32, integer addition is associative, and a threshold that moves in its last bits between runs flips every pixel sitting on it. Four accumulators here were still floats, and they reach the intensity rather than a diagnostic. * The radial background curve. s_radv and rad_sum sum int32 pixel values, so int64 is not an approximation of the old sum, it IS the old sum - and the curve is subtracted from every reflection's background. * The learned profile grid and its second moments, which are sums of (px - bkg) / I over every strong reflection of the frame. There is no exact integer form, so these are fixed point at 2^20: a quantum of 1e-6 of one I-normalised pixel, far below the Poisson noise of the pixel it came from, and some five orders of headroom inside a signed 64-bit accumulator. * The normalisation total in build_profiles, which divides every cell of the profile - 128 lanes on one address, in arrival order. Now summed as integers, exactly, from the grid it normalises. * The fit's own reductions, s_num and s_den among them, which ARE the fitted intensity. These stay float, so fixed point would be a real precision trade over an unbounded range; instead each warp leaves its total in a slot of its own and every thread adds the slots up by warp index. WARP_ATOMIC_ADD is order-independent for the integer accumulators it was written for and not for these, which is what block_sum is for. With the prediction ordering of the previous commit, a run is now reproducible: the same command on the same images writes byte-identical .hkl and .mtz, at -N 1 and at -N 48, on a 16 Mpx rotation set and on a large-cell one. Before, all four differed. The battery is unchanged where it was ever stable: space group identical on all 24 crystals, reflection count on 20, R_meas on 22. The two that move are the two the battery has always seen move between runs of an unchanged binary - which is the point, since they stop moving now. Total 8m02s against 7m55s, inside the noise of per-crystal times quantised to a second. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011n8riB6X59oRjkrSHzNPAU	2026-08-23 10:56:02 -04:00
jungfrauandClaude Opus 5	484a0e162a	Give the predicted reflections an order of their own ... The GPU predictors claim their output slot with atomicAdd(counter, 1), so a reflection's position in the array is whatever order the blocks happened to finish in. That position is not private to the predictor. BraggOwnerKey packs it into the owner map as the tie-break between two centres equidistant from a shared pixel - the map's atomicMin is order-independent, but the number it compares is not - and the ingest and post-refine bucket sorts, whose comparators are deliberately not total, resolve their ties by the order they are handed. So two runs of the same binary on the same images integrated a different set of reflections. Measured on a large-cell rotation dataset: 63301112 observations against 63301139, and 89% of the merged intensities differing by more than 1% of themselves, median 1.8%. Single-threaded as well as at -N 48, which is what ruled out thread ordering and pointed here. Order the downloaded list by (h, k, l, delta_phi) before TruncateToOutput, whose own pick is then reproducible as well. hkl is a property of the reflection rather than of the schedule, and delta_phi separates the two rocking solutions one hkl can have. The CPU predictors already emit in hkl order, so the two paths now agree on it. Sorting a 20-byte key and gathering once, rather than sorting the 88-byte reflections in place, keeps this off the clock: on a crystal predicting some 35000 reflections a frame the run measures 52.2 s against 52.3 s before. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011n8riB6X59oRjkrSHzNPAU	2026-08-23 10:55:37 -04:00
jungfrauandClaude Opus 5	9b1ffbaa71	Allocate a beam-stop shard's accumulators when it is first used ... SetShardCount allocated and zeroed three per-pixel accumulators for every shard up front. With a GPU present none of them is ever written - the frames are decoded and folded on the device - and on a 16 Mpx detector eight shards are 2.9 GB to allocate and clear, measured at 0.8 s of the pre-scan spent on memory nothing reads. A shard now allocates on the first frame that reaches it, and the fold skips shards that never got one. Two things that go with it, not in the version on 2608-performance. Reduce's single-shard fast path returns that shard directly, which is now an EMPTY projection if nothing was ever added to it, where before it was a zeroed full-size one - and both callers index it by pixel. The fast path therefore requires the shard to hold at least one frame; otherwise the general path builds the zeroed projection as before. Also drops a duplicate include of ParallelFor.h. Split out of "Find the first pass's spots on every worker", which carried it as an unrelated rider. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011n8riB6X59oRjkrSHzNPAU	2026-08-23 08:30:17 -04:00
jungfrauandClaude Opus 5	0047d1065e	Read four pixels at a time when flagging strong pixels ... The ring reduction already reads its pixels four at a time; the pass that flags the strong ones still read them one at a time, over the same image. Give it the same quad read. The flag is a per-pixel comparison against a threshold the reduction has already fixed, so nothing is summed here and the result is unchanged pixel for pixel, including the tail the quad read does not cover and the masked pixels it skips. Split out of "Find the first pass's spots on every worker" on 2608-performance, which carried it as an unrelated rider. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011n8riB6X59oRjkrSHzNPAU	2026-08-23 08:30:03 -04:00
jungfrauandClaude Opus 5	74e8b77a0d	Stop scaling and merging what the resolution range excludes ... A crystal integrated to the detector corner but merged well short of it carries observations through the whole merge that the merge then discards. On the heaviest dataset in the rotation test set that is 63.3 M partials of which 6.4 M are ever used: the other nine tenths are sorted, uploaded, scaled, combined and error-modelled before anything looks at their resolution. Ingest copied every one of them unconditionally, and the d_min limit was first applied far downstream, in the ASU grouping. They are now dropped at ingest, immediately after the one big sort: - WHOLE raw-hkl runs are dropped, on the same rawrun_d the ASU grouping already tests. A per-observation test is not equivalent - a run is in or out today by one member's d - and using a different rule here would put the two out of step. - The drop happens AFTER the flux meter, which takes each frame's mean background over every reflection on it, and after the sort, so neither changes. - The compaction runs in index order, so a frame's observations stay contiguous and keep their order, and every per-frame sum keeps its sequence of roundings. The incident-flux divide goes with it: it was reading one int and dividing one float across 5 GB in a pass of its own. The per-frame mean it needs is now accumulated by the ingest fill loop - one frame, one thread, same order, so bit-exact - and the divide rides on the finiteness pass that already touches that field. Ported from 2608-performance with two changes. The ingest fill loop there had been parallelised by an earlier commit that is not being taken, so the mean background is accumulated in the serial loop this branch still has; it is the same sum in the same order either way. And the post-refinement sampling that commit also introduced - thinning the fit to 8 M partials by a hash of the raw hkl - is NOT included. Every consumer of the dropped observations is gated on the ASU group, so dropping them is a no-op for the science; thinning post-refinement is not, its own measurement puts the cell scale breaking at 4 M against a pool of 8 to 16 M, and it makes the fit depend on how far integration ran. That belongs to its own decision. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011n8riB6X59oRjkrSHzNPAU	2026-08-23 08:28:35 -04:00
jungfrauandClaude Opus 5	be73288748	Fit the modulation surface on a grid that spans the detector ... The detector-frame modulation correction takes its 16x16 grid extent from a pass over every full, but the surface is fitted only on the fulls that belong to an ASU group. Those are two different populations, and the gap between them is whatever was integrated past the resolution the merge uses. That made the correction's fate depend on how far integration reached. Cut it back and the grid contracts onto the merged disc while the cell count stays the same, so each cell holds too few reflections, the surface over-fits, and cross-validation throws it away - correctly, on a surface that should never have been fitted at that scale. Varying only the integration limit on one rotation dataset, merged R_meas came out 28.4 / 33.1 / 29.0 / 32.8 / 31.7 %, and the four-point spread is entirely the correction switching on and off: every low value is a run where it was applied, every high value one where it was refused, with no exceptions. Nothing else moved. The grid now spans the detector. Cells with no observations in them keep a factor of 1 and cost nothing, and with integration running to the detector corner - the default - the grid is the one it always was, so the common case is unchanged. On a crystal carrying no resolution limit at all it takes merged R_meas from 39.7 % to 35.5 %. This is a correctness fix in its own right. It also has to come first: without it, any change that narrows the integrated resolution range trips the same over-fit. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>	2026-08-23 08:27:11 -04:00
jungfrauandClaude Opus 5	2eb9780fe2	Weight the corrected intensity, not its factors, in the shared reference ... Folding the fit loop and the score loop into one reference() had to pick one of their two spellings, and it picked the fit loop's: w * I * corr * a, where the score loop had built Is = I * corr * a first and then summed w * Is. Those differ in the last place, and of the two callers it is the score that decides whether a surface is kept at all - so a gate sitting on the fence could go the other way for no reason but the order of three multiplications. Sum w * Is, which leaves the deciding path spelled as it was and matches how the rest of this file accumulates a weighted intensity. The fit's own reference moves by a last place instead; it is iterated to convergence and then scored, so that is the cheaper place to absorb it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011n8riB6X59oRjkrSHzNPAU	2026-08-23 08:26:36 -04:00
jungfrauandClaude Opus 5	ca3ca7170e	Spread the scaling corrections and the space-group search over the cores ... Two thirds of a rotation run is one thread. The image loop is not the problem - on the heaviest crystal of the battery it is 1.8 s of 40 - and neither GPU nor CPU is saturated, because while the corrections and the space-group search run there is one core working and 47 idle. Mean occupancy over the whole run: 3.9 of 48. In the correction surfaces (absorption in the goniometer frame, detector-plane modulation, absorption against time and detector position - all one function): the per-cell accumulation, the score reduction and the final apply are now chunked, as are the three loops that assign a full to its cell, one of which spends a sine and a cosine per full de-rotating it into the crystal frame. Two full sorts of four million floats went with them: only the nine bin edges are wanted, so they are selected instead, each selection starting where the last one left off. The per-group pass is deliberately left serial. The terms of one group are spread all over the list, so the only way to give a thread groups of its own is to walk in group order, and that trades a near-sequential read of the fulls for a random one over a few hundred megabytes - the trade that already lost once in the combine kernel. The space-group search scores each candidate rotation by correlating I(h) against I(Rh) over the whole merge. Every operator it can ask about comes from a fixed list and none of them depend on each other, so they are scored up front, in parallel, and the search reads the cache. The scratch that stops a pair being counted twice is now per worker rather than shared. Worker counts are gated on how much work there is, not on how many cores the machine has (ThreadsForWork). Both parallel helpers start a thread per chunk, so a small dataset on a large node would otherwise pay for 48 thread starts to sum a few thousand terms - and this runs on 8-core laptops as well as on this node. Measured on the heaviest crystal, idle machine, two runs each, summed over both passes: those phases go 7.88 s -> 5.19 s. Whole-run wall time is the wrong ruler for it - it moves +-4 s between identical runs. Battery 9m45s -> 9m23s, space group 21/24, no failures; 16 of 24 crystals bit-identical to the previous run and the rest inside the noise floor of running one binary twice. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>	2026-08-23 08:25:43 -04:00
jungfrauandClaude Opus 5	01b619cfd0	Take the double precision out of the box integrator's inner loops ... boxsum summed its ring background in double and compared each ring pixel against a double threshold. The pixels are integers: a sum of at most a thousand int32 values is exact in a 64-bit integer AND exact in a double, so the two agree bit for bit, and comparing an integer against the floor of the threshold accepts exactly the same pixels as comparing it against the threshold itself. Both loops now do integer arithmetic. That was 39% of the card's double-precision pipe on the development machine and about three quarters of it on the production one, where the double rate is unchanged from Turing while the single rate has doubled - so this is worth more there than here. Alongside it, three things in the combine kernel. rr_nusable was computed by a whole extra walk over every observation and then never downloaded or read by anything. sum_wb and sum_cwb have no F in them, so they are the same in all three reweights and only the last round's values are ever used - two thirds of them were two divisions each, discarded. And CombineParams was the one parameter struct in the file without __restrict__, so the compiler could not assume the observation arrays and the freshly allocated fulls arrays were distinct. Measured on a crystal with 66 million partial observations: boxsum 12.2 s -> 8.3 s, the combine kernel 8.0 s -> 7.6 s, whole crystal 1m17s -> 1m12s. Battery 15m32s -> 9m59s. Same space group on all 24 crystals, none failed. Two things measured and NOT kept, recorded so they are not tried again: sorting the raw-hkl runs by length so a warp holds runs of similar length - it trades away the locality of neighbouring runs in the permutation and came out slower (7.6 s -> 8.8 s); and page-locking the integrator's host staging arrays individually - eleven separate registrations of small heap allocations overlap on shared pages and the driver refuses them. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-23 08:24:21 -04:00
jungfrauandClaude Opus 5	a8cca3e5d4	Parallelise the incident-flux divide, drop a redundant sync ... DivideOutIncidentFlux was still the last fully serial pass in Ingest: a sweep over every observation to take each frame's mean background, and another to divide every rlp by its frame's flux. Ten gigabytes of traffic on one thread. The per-frame means go a frame at a time rather than an observation at a time, so each frame's running sum stays in one thread and in the order it had - splitting by observation would cut a frame across two threads and the partial sums would have to be recombined, which is a different sequence of roundings. The divide is per-element and splits anywhere. The adaptive spot finder synchronised after flagging strong pixels. The extractor that reads those pixels runs on the same stream, so the ordering already guaranteed the flagging had finished; the wait only idled the host, once per image. Measured on a crystal with 66 million partial observations: Ingest 8.5 s and 7.7 s -> 7.1 s and 6.6 s, whole crystal 1m24s -> 1m17s. Merged statistics unchanged. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-23 08:24:16 -04:00
jungfrauandClaude Opus 5	8ae53b7fdf	Say what actually makes the post-refine bucket sort reproducible ... The bucketing commit justified itself with "the partials order became total in an earlier commit", which is true of the scale/merge ingest and not of this sort: part_less ends at the image number, so two partials of one reflection on one image tie, exactly as they did before. Nothing is wrong with the result. The counting-sort prefix lays each bucket out chunk by chunk, and a chunk is a contiguous span of the gathered order, so every bucket arrives at std::sort in global gather order no matter how many threads scattered it - the order is reproducible run to run and identical across -N. Giving Partial a rank field to make the comparator total would settle those ties by index instead, at eight more bytes on an array that reaches tens of millions of elements, and would change nothing anyone can observe. So state the invariant where the comparator is, rather than leaving the next reader to trust a claim that does not hold for this half. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011n8riB6X59oRjkrSHzNPAU	2026-08-23 08:23:57 -04:00
jungfrauandClaude Opus 5	01d16231b3	Sort the partials and the post-refine events in buckets, in parallel ... Both were one std::sort on one thread over tens of millions of elements, and together they were a third of a crowded crystal's run. Bucketing by h first makes them parallel. h is the comparator's leading key, so the sorted array is exactly the buckets laid end to end, and each bucket sorts on its own thread. In Ingest the keys are built straight into their bucket slot, so this replaces the build pass rather than adding one and the packed-key array is never duplicated; the extra memory is a few hundred kilobytes of histograms. Buckets are taken largest first, because the tail of the phase is whichever bucket finishes last. The run split falls out of the same structure for free: a run of equal (h,k,l) never crosses an h boundary, so each bucket counts its own runs, a scan over the buckets gives the offsets, and the arrays are sized exactly - which also removes the repeated growth the push_backs were paying for. The h range comes from the finiteness pass, which already reads every observation. The partials order became total in an earlier commit, when the observation index was added as the last key. That is what makes this safe rather than merely fast: the permutation is uniquely determined, so a bucket sort produces the same one a single sort would. Measured on a crystal with 66 million partial observations: Ingest 15.2 s and 14.3 s -> 8.3 s and 7.4 s, the post-refine event sort out of the top ten gaps entirely, the whole crystal 2m22s -> 1m24s. Battery 15m32s -> 10m05s. Same space group on all 24 crystals, none failed, and no crystal's R_meas moved by more than 0.3 points. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-23 08:22:40 -04:00
jungfrauandClaude Opus 5	c1b85c7e88	Reduce within the warp before the Bragg integration atomics ... fit and boxsum were 80% of GPU time on a crowded crystal - 78 s of it. Neither was bandwidth- or occupancy-bound: both sat at about an eighth of the issue rate the card can sustain, stalled. What stalls them is the block-wide accumulations. Every one has all 128 lanes of the block adding into one shared address, and a shared-memory atomicAdd on a float or a 64-bit integer has no instruction on either Turing or Ada - it compiles to a compare-and-swap retry loop. So those 128 lanes serialise into 128 retries, eighteen times per thread in fit. Summing across the warp first and letting one lane do the atomic leaves four per block instead of 128. That is the whole story: the arithmetic below was worth 2%, the atomics 5.6x. The arithmetic is still worth having, and is what was expected to matter: - compute_shell ran on all 128 threads of a block for a value that belongs to the reflection. It is two software double-precision divisions, on a card whose double throughput is a thirty-second (a sixty-fourth on the production one) of its single. One thread does it now. - The Kabsch inner loop divided by the same weight three times; the compiler emits the whole correctly-rounded sequence each time. One reciprocal now. Likewise the two Gaussian widths and the profile normalisation, which are constant over a reflection's cells and were divided per cell. - boxsum read the pixel before deciding whether it wanted it. The window is the bounding box of an ellipse, so nearly half of it is neither the signal disk nor the background ring, and those slots were fetching a cache line for nothing. Measured: fit 50.8 s -> 9.1 s, boxsum 27.5 s -> 12.1 s. A crowded crystal 2m22s -> 1m58s, a 16M-pixel one 39.5 s -> 37.2 s, the whole battery 12m30s -> 11m35s. Same space group on all 24 crystals, none failed. The integer sums are unchanged - addition is associative. The float ones move in their last bits and become more reproducible, since a fixed shuffle tree replaces whatever order the atomics arrived in. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-23 08:22:16 -04:00
jungfrauandClaude Opus 5	52756273e1	Make the partials order total, and hoist 1/sigma out of the IRLS loop ... The sort that orders every observation by (h,k,l,image_number) was not a total order: two observations can genuinely share all four. The predictor emits BOTH intersections of a reflection's rotation circle with the Ewald sphere, and near the blind region - where zeta is smallest - the two are close enough in angle that both are accepted on the same frame. Which of them came first was then whatever the sort happened to produce. That was observable. The combine takes on_ice from the FIRST member of a rocking event, so the order decided whether a full was flagged as ice at all, and its per-event sums are floating point, so it moved intensities in their last bits. The observation's own index is now the final key, which orders them by arrival - and, more usefully, makes the order unique, so it no longer depends on which algorithm sorted it. sigma never changes once it is uploaded, so 1/sigma is the same in all thirty IRLS iterations of all three scaling iterations of all five scaling passes. It was being recomputed every time: a 64-bit reciprocal is a hardware estimate plus five refinement steps, and the profile put the three divisions in that loop at 21 of its 31 double-precision instructions. It is computed once now, in the pass that already streams every observation. The CPU has always hoisted it; this is the GPU catching up. Same expression on the same operand, so the value is what the loop used to compute, bit for bit. Also: PrepScaleObsKernel is not a grid-stride loop, but the scale-fulls path capped its grid at 65535 blocks like the grid-stride kernels around it. Above 16.8 million fulls that silently left the tail of sco_coeff/sco_ok stale. No dataset here reaches it; the cap is simply wrong for that kernel. And the AoS-to-SoA staging that feeds the GPU - the widest pass in Ingest, reading an 80-byte struct and writing fourteen arrays out of it - ran on one thread. Full 24-crystal battery: same space group on all 24, none failed, one crystal moved R_meas by 0.8 points with CC unchanged (it moves by that much between runs of an identical binary). 15m32s -> 13m35s. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-23 08:22:16 -04:00
jungfrauandClaude Opus 5	594100accc	Make the rotation-scale fit reproducible, and stop refining past a float ... Two follow-ups to the closed-form fit. The five per-fifth sums were reduced under a mutex, so the order in which the chunks were added depended on which worker reached the lock first and the fitted scale moved in its last bits between runs of the same binary. Each chunk now folds into its own slot and the slots are summed in chunk order, which is the reduction pattern the rest of the analysis code uses. The split ParallelChunks makes is fixed, so the sum is now the same sequence every time. The golden section bracketed to 1e-9. The fit is narrowed to a float before it is applied, and a float's epsilon is 6e-8, so the last ten or so iterations - each a full parallel pass over every event - refined digits that are discarded on the next line. Bracket to 1e-7. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011n8riB6X59oRjkrSHzNPAU	2026-08-23 08:22:00 -04:00
jungfrauandClaude Opus 5	c4c2d598d7	Fit the goniometer rotation scale in closed form ... The fit has ONE parameter, and it was handed to Ceres as one residual block per rocking event - 8 million of them on a large crystal. Each block is a functor, an auto-diff cost function and a loss object on the heap, and the solver then factorises an 8-million-by-one Jacobian on every iteration. It cost 13.7 s. The residual is closed-form in k. A rotation preserves length, so |p_lab| is |e_mid| whatever k is and only the z component moves; Rodrigues gives it exactly: r(k) = C + A cos(a k) - B sin(a k) = C + R cos(a k + psi) C = lambda |e|^2 / 2 + u_z (u.e), A = e_z - u_z (u.e), B = (u x e)_z with a the event's angle from the sweep centre. That is the same function the functor computes - Ceres uses the exact Rodrigues form here, so there is no small-angle branch to disagree with - and it reduces the fit to minimising a smooth function of one variable over the interval the solver was bounded to. It is scanned on a grid and then closed in by golden section; the objective's curvature jumps wherever an event crosses the Huber knee, which is why this is not a Newton iteration. The coefficients are computed in double and stored narrowed. Their rounding moves the minimiser by ~1e-10, and k is carried downstream as a float, so the committed value is the same to far more digits than anything reads. One pass over the events yields the five per-fifth partial sums, so the all-data fit and the five leave-a-fifth-out folds share it. That matters because the jackknife only runs when the fit is big enough to act on, and on a crystal that trips it the old code paid for six full solves. The partials gather ahead of it counted first and then filled instead of growing one vector by push_back tens of millions of times, which copied the whole thing on every doubling. Measured: unchanged verdict and k to five decimals on the regression crystals. Full 24-crystal battery: same space group on all 24, none failed, 15m32s -> 13m35s together with the scale/merge changes. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-23 08:20:48 -04:00
jungfrauandClaude Opus 5	c3d3161af0	Fold the beam-stop batch before its frame size changes ... ShadowAccumulatorGPU::Add sized the raw buffer before closing the pending batch, and EnsureRawCapacity assigned frame_bytes on entry. FoldPending strides `raw` by frame_bytes, so a frame of a different size arriving mid-batch made the already-decoded frames fold with the new stride: every pixel of the pending batch read from the wrong offset, silently, with no error. The depth-change branch that exists to handle exactly this ran one step too late to help. Fold first, then resize, then adopt the new stride. The batch also closes on a change of frame size, not only of pixel mode - a batch is one layout, and the mode alone does not fix the layout. The decoder was likewise built once from the first frame and never rebuilt, so it is now rebuilt when the frame size changes; without that the mixed-size path this commit repairs would still decode into a buffer of the wrong size. Also calls Gpu() once in ShadowFinder::AddImage instead of twice - it takes and releases a mutex each time, once per image. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011n8riB6X59oRjkrSHzNPAU	2026-08-23 08:20:37 -04:00
jungfrauandClaude Opus 5	ddf625d833	Decode and accumulate the beam-stop projection on the GPU ... The pre-scan decompressed its frames on the host and folded them into a per-pixel projection there. On a 16M-pixel detector that is 60 frames of 72 MB to decompress and 20 bytes per pixel to read and write back per frame - about 40 GB of memory traffic - and it was the whole cost of the phase once the mask was no longer the bottleneck. Only the compressed chunk crosses PCIe now. BSLZ4DecoderGPU already exposes the raw decoded bytes (Decode(), the path its own tests use), which is what this needs: the projection is defined on the RAW STORED COUNTS with the pixel type's sentinel skipped, not on the preprocessed image, so nothing here goes through the preprocessor. Sums, maxima and counts are integers, so the device result is identical to the host's rather than merely close. Frames are folded in batches of four. The fold reads and writes the whole accumulator whatever the batch holds, so per frame it was spending most of the bandwidth on the accumulator rather than on the data; four is where that stops mattering, and every frame beyond it is another full frame of device memory, which costs more in cudaMalloc - device-synchronizing - than it saves. The accumulator is built on a thread of its own. It allocates and clears several hundred megabytes, and doing that in the constructor stalled the caller before it had read its first frame. Frames the device cannot take - anything but bitshuffle+LZ4 - still go to a host shard, so a run mixing compressions needs no second code path, and a build without CUDA is unchanged. RotationScaleMergeGPU set the CUDA device in its constructor and never put it back. CUDA's current device is per-thread, so that silently re-pinned the calling thread for the rest of its life, and the destructor freed several gigabytes against whatever device happened to be current by then - CudaDevicePtr records no device of its own. Every entry point now sets the device on entry and restores it on exit. ParallelFor/ParallelChunks moved to common/ParallelFor.h; two files had copies and a third wants them. Measured on a 16M-pixel rotation dataset: pre-scan 4.78 s -> 2.37 s -> ~2.0 s, shadow unchanged at 139126 pixels (22143 on a 2M-pixel dataset). Full 24-crystal battery: same space group on all 24, none failed, 15m32s -> 14m49s. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-23 08:19:20 -04:00
leonarski_fandClaude Opus 5	83b33e19ee	Give each FFT direction a block and its histogram shared memory ... Cherry-picked from 2608-performance, restricted to the indexer: the same commit there also hoists a reciprocal out of a loop in the scaling code, which is not being touched on this branch. The histogram bins are unsigned integers and the counts stay below 2^24, so they convert to float exactly - the vote is bit-identical, and the indexing result with it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01VfYvJT5Nb71suJCowRBn5z	2026-08-23 13:12:49 +02:00
jungfrauandClaude Opus 5	20ef59205b	Build the GPU engines a worker never uses on first use, not always ... Every worker thread built a full set of analysis engines. Two of them are never asked for on the offline path: the fixed-threshold spot finder, because detection is adaptive by default, and the azimuthal integrator, because the fused adaptive finder produces the profile as a by-product. They are still needed elsewhere - the broker defaults to non-adaptive detection, and --no-adaptive-spots asks for the finder - so they are built on first use rather than removed. A lazily built finder takes the current resolution mask on construction; without that it would find spots outside the limits it was never told about. The bitshuffle decoder sized its output buffer for the widest pixel type there is rather than the one the images actually have, holding a second full frame per worker on 16-bit data. It is sized from the image now and grows if a later frame needs more. The shared-table checksum runs over eight interleaved lanes. FNV's multiply is a loop-carried dependency, so one chain retires a byte every few cycles whatever memory bandwidth is spare, and every worker hashes tens of megabytes of geometry tables as it builds its engines - about 5% of all CPU samples on a 16M-pixel detector. Measured on a 16M-pixel rotation dataset: cudaMalloc 11314 -> 9474 calls and, with cudaFree, 117 s -> 78 s of aggregate thread time; both synchronise the whole device, so that time is spent blocking every other worker. Whole battery 15m32s -> 12m30s. Data quality against main, over 24 crystals and eight statistics each: the same space group on all 24, and every difference smaller than what two runs of an IDENTICAL binary produce (measured: 13 of 24 crystals reproduce exactly run to run, worst R_meas swing 5.5 points, against 4.6 points for main vs this branch). The float atomics in the reductions have always made this so. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-23 13:12:36 +02:00
jungfrauandClaude Opus 5	495e2d752d	Read four pixels at a time in the ring reduction ... reduce_rings_shared was 69% of all GPU kernel time - 116.8 s of a 70 s run across four cards. It is not bandwidth bound: flag_strong streams the same two arrays through the same grid-stride loop and reaches 196 GB/s, while this reached 30. The difference is the shared-memory atomics. Lanes in a warp read consecutive pixels along a detector row, a ring is a few pixels wide, so most of a warp lands in a handful of rings and the atomics to each one serialise. Two changes. The block reads four pixels per thread as one 16-byte and one 8-byte transaction, and merges the ones that fall in the same ring in registers before touching shared memory. Consecutive pixels usually DO share a ring, so this is where the win is: a run costs one set of atomics instead of one per pixel. npix is not guaranteed to be a multiple of four - it is width x height on the converted path, and detectors are not obliged to be even - so the vector loop stops short and a scalar loop finishes the remainder. Reading past the end would not fault, which is worse than if it did: it would fold uninitialised device memory into the accumulators and move the detection threshold in a way that does not reproduce. And the grid is sized from the occupancy the device reports, per pass. The two passes have different shared footprints - the first carries the corrected rings as well - so they do not fit the same number of blocks, and a grid sized for one left the other running a second wave at a quarter occupancy. The comment that justified the old grid reasoned from 1536 threads per SM, which is an Ada number; the card it ran on holds 1024. The run totals are still exactly what they were. The accumulators are unsigned 64-bit, so summing a run in a register and adding it once is the same value as adding each pixel separately - addition mod 2^64 is associative, overflow included - which is what keeps the ring statistics, and therefore the detection threshold, independent of how the work was grouped. That is the property the integer accumulators exist for. (The run accumulators are unsigned for the same reason: signed overflow would be undefined, and four squares of a large pixel value reach 2^64.) The corrected float sums, which feed the reported profile rather than any decision, change in their last bits as they already did between runs. Measured on a 16M-pixel rotation dataset: the kernel 116.8 s -> 19.1 s (6.1x), no longer the largest; the whole run 70 s -> 39.5 s. Full 24-crystal battery: same space group on all 24, none failed, 15m32s -> 12m47s. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-23 13:12:36 +02:00
jungfrauandClaude Opus 5	670831bad4	Stop allocating GPU and pinned memory nothing reads ... Three resource fixes and two latent bugs, none of which changes a computed number. The preprocessed image has a host copy that only a CPU engine ever reads. On the GPU path every engine reads the device buffer instead, and rugnux always runs the fused adaptive finder, so that host copy is allocated, zeroed and PAGE-LOCKED for nothing - 72 MB per worker, 3.5 GB over 48 of them, and a cudaHostRegister each, which the driver serializes. It is now skipped by the same condition that already decides whether the device copies the image back. ImagePreprocessorBuffer keeps the pixel count separately so size() still answers when the mirror was not allocated. ROIIntegrationGPU asked device 0 for the SM count it sizes its grid from, while workers are pinned round-robin across the GPUs - so on a multi-GPU node it could size a grid from a card it never launches on. It asks the current device now, like every other engine. ~CudaRegisteredVector called a function that throws out of a destructor, and the move-assignment did the same from a noexcept function. Either would abort the process rather than report the failure, and teardown - after a device reset, or while another exception unwinds - is exactly where cudaHostUnregister fails. Both now use an unchecked unregister, as every other destructor in that header already does for its own teardown call. The throwing form stays for rebind()/unregister(), which are called from live code. Measured on a 16M-pixel rotation dataset: unchanged space group, merged reflection count and merging statistics. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-23 13:12:36 +02:00
leonarski_fandClaude Opus 5	b74d8f8545	Give ParallelFor a home and a test ... The two shapes - a fixed contiguous split, and work stealing off an atomic - had been copied into whichever file wanted them: an anonymous namespace in RotationScaleMerge.cpp, and another, byte for byte the same, in ShadowFinder.cpp, whose comment claimed it was "the only other file that wants it". The header is taken from the beam-stop GPU commit on the performance branch, which is not otherwise being picked. ShadowFinder now uses it, so the construct is exercised rather than shipped unused, and its own copy is gone. The beam-stop mask is unchanged, which its reference count already pins. Tested for the properties the callers rely on and which are easy to lose in a rewrite: the chunked slices tile the range in order with no empty one, work stealing visits every item exactly once, one thread means the caller's loop in order, an empty or negative count does nothing, an exception in a worker reaches the caller, and - the point of the whole thing - the answer is the serial answer bit for bit at every thread count. RotationScaleMerge.cpp keeps its own copy for now; consolidating it belongs with the scaling work, which is not being touched here. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01VfYvJT5Nb71suJCowRBn5z	2026-08-23 13:05:31 +02:00
jungfrauandClaude Opus 5	996cd20106	Make the beam-stop mask O(pixels) and parallel ... GetMask() was 3.28 s of the 4.78 s pre-scan on a 16M-pixel detector, all on one thread. Four changes, none of which alters the mask: dilate() was a multi-source BFS. On a full rectangle with no obstacles the 8-connected graph distance IS the Chebyshev distance - a path stepping towards the target never has to leave the frame - so the result is a dilation by the (2r+1) square clipped to the frame, which separates into a pass along x and a pass along y. That is O(1) per pixel whatever r is, with no queue and no 4-bytes-per-pixel distance array (72 MB, allocated and filled five times per call). The erode() case is the one that hurt: it dilates the COMPLEMENT, so on a detector whose shadow is under 1% of the pixels it seeded the BFS from essentially every pixel. fill_holes() floods the background from the border. It now floods the bounding box of the region grown by one: everything outside that box is background and the box's own ring is background, so the whole outside is one border-connected component and a background pixel inside the box is border-connected exactly when it reaches the ring. The three baseline iterations re-binned every pixel by radius and re-took a median each time. The iteration only ever excludes pixels whose background is below a cut, and dividing by a positive baseline is monotone, so a ring's excluded pixels are exactly its lowest ones and the next median is an order statistic of the same, unchanging ring. The rings are binned and sorted once; each iteration then picks a rank and counts a prefix. Nine full-image passes become one. box_sum's vertical pass walked one column at a time, striding a whole row per step and missing on every access; it now carries a strip of columns together. Each row's and each column's running sum keeps its terms in its order, so the floating-point rounding is unchanged - only the traversal differs. The pooled COUNT is a count of at most 25 pixels, so it is an exact integer box sum now rather than a floating-point one; the background itself stays in double, because its running sum adds and subtracts across a whole row and in float the two roundings would not cancel. The per-pixel passes then run on all threads, and GetMask takes a thread count. Measured on a 16M-pixel rotation dataset: GetMask 3.28 s -> 0.99 s, whole pre-scan 4.78 s -> 2.37 s, whole run 1m10s -> 1m03s. The mask is unchanged on both a 16M and a 2M-pixel dataset (139126 and 22143 shadow pixels), as are the space group, the merged reflection count and the merging statistics. Also corrected the comment on erode(): the dilation cannot seed outside the frame, so outside behaves as foreground, not as complement. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-23 12:50:12 +02:00
jungfrauandClaude Opus 5	51c628af3b	Parallelize the beam-stop pre-scan ... The pre-scan read its sample of frames in a plain serial loop: one thread did the HDF5 read, the decompression and the full-detector accumulation for every frame. The cost is fixed per frame rather than per dataset, so it grew straight with detector area - measured at 0.9 s on a 2M-pixel detector and 7.9 s on a 16M-pixel one, where it was 11% of the whole run with 47 of 48 cores idle. Frames are now read on several workers. ShadowFinder keeps one projection per worker so nothing is locked while an image is added, and the projections are summed when the mask is read; the sums and counts are integers, so the result does not depend on how the frames were spread over the workers. A shard that never counted a pixel is skipped when the maxima are merged - it holds 0, which would otherwise beat a genuinely negative maximum. Worker count is capped (PRESCAN_MAX_WORKERS): a shard costs 20 bytes per pixel, and the accumulation is memory-bound, so a handful of workers already saturates it. The beam-centre spot pool is stitched together in sample order after the workers join, so frame numbering and the spot list are what the serial read produced regardless of how the workers interleaved. A frame still joins the pool only if it could be read. ShadowFinder::AddImage took its decompression scratch buffer BY VALUE, so the caller's buffer stayed empty and every frame allocated and zero-filled a fresh full-size uncompressed image (72 MB on a 16M-pixel detector) and freed it again. It takes a reference now, and each worker reuses one buffer. Measured on a 16M-pixel rotation dataset: pre-scan 7.9 s -> 4.8 s, whole run 69.2 s -> 65.1 s. Results are unchanged - same shadow pixel count, same space group, same merged reflection count and merging statistics on both a 16M and a 2M-pixel dataset, and the beam-centre path still commits the same centre. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-23 12:50:07 +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	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	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	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	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
leonarski_f	239a441ee6	v1.0.0-rc.140 (#50) ... 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: For DECTRIS detectors, ZeroMQ link is persistent, to save time for establishing new connection * jfjoch_broker: Minor bug fixes for rare conditions Reviewed-on: #50	2026-04-29 21:40:22 +02:00
leonarski_f	4878318c27	v1.0.0-rc.139 (#49) ... 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: Further reduce startup time for DECTRIS detectors by selectively modifying SIMPLON parameters on `/start` * jfjoch_broker: Further reduce startup time for DECTRIS detectors by not setting beam center and detector distance via SIMPLON API on '/start' * jfjoch_broker: Add an extra message to ZeroMQ puller ready to monitor Lite worklow preparation time * jfjoch_broker: Image buffer configuration is postponed for Lite receiver flow till start message is received * jfjoch_broker: Use nanoseconds internally for frame/image/readout time * jfjoch_broker: Extra messages added for receiver operation (to be removed after debugging finished) * jfojch_broker: Improve profiling of different data analysis steps * jfjoch_broker: Record integration reflection count * jfjoch_broker: Fix bug where ZeroMQ preview frequency was confusing time units (micro vs. milliseconds) * jfjoch_broker: Fix bug where '/wait_till_done' got deadlocked * jfjoch_writer: Fix confusion between NaN and zero in floating-point datasets **Breaking changes**: detector definition is now using nanoseconds to define minimum frame time, minimum count time and readout time. Reviewed-on: #49	2026-04-29 09:50:50 +02:00
leonarski_fandtakaba_k	230480e390	v1.0.0-rc.138 (#48) ... 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: Cleanup DECTRIS start-up code to enable a shorter start time jfjoch_broker: Allow for asynchronous start to allow overlapping detector configuration with other beamline preparations jfjoch_broker: Goniometer axis name is converted to lowercase jfjoch_broker: Fix bug, where wrong HTTP error codes were returned jfjoch_broker: Improve sigma estimation during merging (K. Takaba) --------- Co-authored-by: takaba_k <kiyofumi.takaba@psi.ch> Reviewed-on: #48 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-27 19:56:14 +02:00
leonarski_f	c981e1b91c	v1.0.0-rc.137 (#46) ... 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: Better track time for each operation in the processing stack * jfjoch_broker: Rewrite preprocessing of diffraction images in the non-FPGA workflow to better use GPUs (work in progress) * jfjoch_broker: Remove ROI calculation in the non-FPGA workflow (work in progress) * jfjoch_viewer: Toolbar displays image number starting from 1 (instead of 0) Reviewed-on: #46	2026-04-25 19:59:21 +02:00
leonarski_f	c1c170112c	v1.0.0-rc.136 (#45) ... 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 logic regarding indexing architecture and thread pools (work in progress). Reviewed-on: #45	2026-04-20 11:54:33 +02:00
leonarski_f	bb9f5c715f	v1.0.0-rc.135 (#44) ... 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. * Multiple small bug fixes scattered across the whole code base. (detected with GPT-5.4) * jfjoch_viewer: Improve image render performance Reviewed-on: #44 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-16 11:59:59 +02:00