379 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	ab14ca10e8	Reindex into the ASU: follow the change of hand, not the hand landed on ... ReindexMergedIntoAsu swapped I(+)/I(-) whenever the reindexed index came out on the minus side of its Friedel pair. That is right only for a row that started on the plus side, which is every row when merge_friedel is set - and none of the problem cases. With the mates kept apart, the merge stores the plus mate at +hkl_asu and the minus mate at -hkl_asu (Merge.cpp), while RotationScaleMerge attaches I_plus / I_minus in the plus convention on both rows alike, keying the lookup at plus=true. An alternative-indexing operator is rotation-type, so op(-x) == -op(x) and the two mates always land on opposite sides: testing key.plus alone therefore swaps exactly one row of every pair, whichever way the operator went. The pair ends up self-contradictory, and the mmCIF's pdbx_I_plus / pdbx_I_minus and the F(+)/F(-) columns are swapped on half the rows. Reached by "rugnux -A --model model.pdb" - -A clears MergeFriedel - on a crystal whose indexing ambiguity the model resolves, which is the one path that both keeps the mates apart and reindexes. The swap now fires on was_plus != key.plus. With merge_friedel every row is stored at the ASU representative, so was_plus is always true and this reduces to the previous test; the existing change-of-hand case is unchanged. The test that covered the merge_friedel=false path checked only I, so it passed either way. The new one builds both mates of a pair and asserts they still agree about which intensity is which afterwards - an invariant that holds however the operator moves the hand, so it fails on the old code for either direction. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016L1qig74oYQzfUJJZbbxFh	2026-08-27 16:04:37 +02:00
leonarski_fandClaude Opus 5	bc500d1578	rugnux: report what --model found, and attribute GEMMI's bundled headers ... Two things left open by the previous commit. A model that was validated left nothing in the results report. R-work, R-free, the bulk-solvent parameters and the map filenames went to the log and nowhere else, so a run given --model was, in the file anyone reads afterwards, indistinguishable from one that was not - and the WARNING line added last commit was the only trace of a model that failed. Section 10. MODEL VALIDATION now carries it: MODEL_FILE, the space group the model is in, R_WORK / R_FREE with their reflection counts, the bulk-solvent k_sol / b_sol and overall scale, the mean 2Fo-Fc density at the atom centres, the hand and indexing operators the written reflections were brought into the model's frame with, and MAPS_PREFIX. A model that could not be used gets MODEL_VALIDATION= NOT_PERFORMED and the reason instead, in the shape the merging section already uses. A run that asked for no model has no section at all. That moves WARNINGS from 10 to 11, which is what REPORT_VERSION is for: it is now 4. No existing key was renamed and no table column moved, so a consumer that greps for what it needs is unaffected; one that keys on the section number of WARNINGS is not, hence the bump. The four third-party headers GEMMI has always bundled - fast_float, half, pocketfft and tinydir - were never listed in THIRD_PARTY_NOTICES.md, riding instead under GEMMI's single MPL-2.0 row. They are other authors' code under other licences (Apache-2.0 OR MIT OR BSL-1.0, MIT, BSD-3-Clause, BSD-2-Clause), and MPL-2.0 does not speak for them. Each now has its own row and its own licence text, alongside the PEGTL and sajson entries added with the CIF parser, and a note records why the six are listed separately from GEMMI. Their terms live in the headers rather than in LICENSE files, so five of the six texts are kept by hand; COLLECT.sh says so and copies the one - PEGTL - that ships a file. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016WmryXe8ASbNi632sUMfsa	2026-08-27 13:50:13 +02:00
leonarski_fandClaude Opus 5	2e8040c60c	rugnux: read mmCIF models with --model, and say when a model could not be used ... --model called gemmi::read_pdb unconditionally, so a coordinate file in mmCIF - which is how the PDB serves coordinates by default - was refused outright: Model validation: cannot read model 6G8A.cif: Incorrect file format (perhaps it is cif not pdb?) Worse than the refusal was what followed it. ValidateAgainstModel logged, returned an empty result, and the run went on to finish with exit code 0, no R-free, no maps and nothing in the report - indistinguishable from a run that was never given --model at all. A script that passed a .cif, checked the exit code and grepped for R-free simply got nothing back. Both read sites now go through read_structure_gz with CoorFormat::Detect, so PDB, mmCIF and mmJSON are all read, gzipped or not, and the format comes from the file's content rather than from its name. Detect is passed explicitly: GEMMI otherwise takes the extension and only falls back to the content when it does not recognise one, and a model arrives named however whoever produced it named it. That needed a part of GEMMI the vendored subset had trimmed away. mmread.hpp was already here but its CIF parser was not, so this restores what upstream GEMMI ships: read_cif/mmcif/json/mmread_gz, plus GEMMI's own copies of PEGTL (MIT, Colin Hirsch and Daniel Frey; 155 headers, 672 kB) and sajson (MIT, Chad Austin; one header). Both are listed in THIRD_PARTY_NOTICES.md with their own licence texts, PEGTL's collected by COLLECT.sh and sajson's kept by hand, its terms being a comment block rather than a file. json.cpp carries a one-line change: upstream keeps sajson at the root of its repository, outside the include tree this subset copies, so the include points at where the other bundled headers live. ModelValidationResult gains failure_reason, and a model that was asked for and could not be used now reaches the results report as WARNING: Model validation did not run: model bogus.pdb has no atoms or no unit cell in --mode mx and --mode scale alike. The run still succeeds - a merge that is good is not made bad by a model that was not - but it no longer does so quietly. One log line was making a claim it could not support: the indexing-ambiguity message said the ambiguity was "resolved against the supplied model" while being printed before the model is read, so it announced a resolution that a failed model never performed. It now says the model will be used; the reference branch, where the work really has already happened, keeps the past tense. Verified on the rotation test dataset with a deposited mmCIF, the same file gzipped, an mmCIF under a .pdb name, a PDB, and an unreadable file. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016WmryXe8ASbNi632sUMfsa	2026-08-27 13:42:48 +02:00
leonarski_fandClaude Opus 5	e65cfdc675	rugnux: record in the report how the run was invoked, what it cost and what it ran on ... The results report said what the run determined but nothing about how it was produced, so a report read next to a lost shell history could not be reproduced or compared. Four keys in the header block, all new, none renamed - a consumer that greps for what it needs is unaffected, so REPORT_VERSION does not move: COMMAND_LINE= rugnux -o myrun --model model.pdb dataset_master.h5 WALL_TIME= 262.41 GPU_COUNT= 4 GPU= 4x NVIDIA A100-SXM4-80GB The command line is argv as one shell-ready line; an argument that would not survive being pasted back into a shell is single-quoted, so a file prefix with a space comes back as the one argument it was. It replaces the raw argv echo at the top of the run, which had no quoting at all. WALL_TIME is the whole invocation, timed from the top of the CLI. It is deliberately not result.total_time_s, which starts inside Rugnux::Run and so counts neither opening the file nor setting up the analysis - and which --mode scale never sets at all, having no ProcessResult of its own. It is printed on stdout as well, next to the processing time it is slightly larger than. The GPUs are the reason rugnux is fast, and until now nothing said whether any were being used. get_gpu_names() reports them per device and get_gpu_description() collapses repeats, so four identical cards read as one line rather than the same name four times and a mixed machine keeps one group per model. Both have a CPU-only implementation, so the JFJOCH_USE_CUDA=OFF build reports GPU_COUNT= 0 rather than failing to link. The same line is printed at startup, before the run rather than after it: a machine that turns out to have no GPU - a driver mismatch, a CUDA_VISIBLE_DEVICES left over from another job - is worth knowing about while there is still time to stop, not once the run has taken an order of magnitude longer than it should. GPU_COUNT= 0 is written with no GPU= line beside it, because the absence is the statement. The header comment claiming timing is deliberately absent from the report is now wrong and says so: rates and per-image costs stay on stdout, the total does not. Verified on the rotation test dataset in both build configurations, with and without CUDA_VISIBLE_DEVICES, in --mode mx and --mode scale. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016WmryXe8ASbNi632sUMfsa	2026-08-27 13:09:54 +02:00
leonarski_fandClaude Opus 5	5f838bdb26	Broker: refuse a run the writer cannot write before arming the detector ... A writer refusing to overwrite an existing file was reported badly, and the earlier fix only covered half of it. The commit message of a6a715703 states the assumption that broke: "SendStartMessage precedes every std::async in the receiver constructor". That is true of JFJochReceiverFPGA, where the start message goes out from the constructor body, and false of JFJochReceiverLite, where it goes out from MeasurementThread - launched by std::async from the constructor, which waits only on data_analysis_started. On the DECTRIS path the writer's refusal therefore cannot reach services.Start(); it arrives from services.Stop(), i.e. the second try-block of the state machine's MeasurementThread, which never touched start_exception. /wait_till_done answered 200 for a run that never wrote anything. Two changes, in front of the problem and behind it. In front: a PREFLIGHT frame (TCP protocol version 3 -> 4), sent to every writer before the receiver is built and before the detector is armed. It carries the same CBOR start message a START does and asks one question: could this run be written? The writer runs FileWriter::Preflight - the first three statements of the FileWriter constructor, stopping short of the only one that creates anything - and answers with an ACK. Shared code, so a pre-flight that passes cannot be contradicted by the start behind it. A refusal is not fatal: nothing was started, the connection stays usable, and above all no series is left armed waiting for a trigger that will not come. Both ends already reject a frame of another protocol version, so the bump costs no compatibility. The check now covers the data files, not only the master. A stale _data_000001.h5 used to sail through and fail when the file was renamed into place at the end of the run, after the whole dataset had been collected. The writer holding the master file checks for all of them - they share a directory by construction, the master linking them by relative name - so the siblings do not race each other statting files the others are creating. Behind: /wait_till_done maps an Idle state to 200 or 500 by the severity of the end-of-run message, so a collection that lost packets, or whose writer could not write, is no longer indistinguishable from a good one to a script. A cancelled collection is not affected - MeasurementThread checks the cancel before it looks at the completeness of the data, and reports it with Info severity - and a warning is still a 200. start_exception is untouched. The PREFLIGHT payload is built from FillMessage alone, which is what keeps it small: the per-pixel arrays are added by SendStartMessage and are not in it. Measured on a JUNGFRAU 9M, 1.4 kB against 543 kB for the start message. It is deliberately the whole of FillMessage rather than the fields the check reads today - a hand-picked subset would answer for a different set of file names the day the check learns to read one more field, and would do it silently. Three defects found on the way: TCPImagePuller republished a PREFLIGHT as a real start message, announcing to downstream consumers a run that was not going to happen. TCPStreamPusher::run_number was a plain uint64_t written by the control thread and read by every ACK thread; Preflight adds a second writer to it. StreamWriter::CollectImages reprocessed the last frame whenever WaitForImage returned false - run is only tested at the top of the loop - so an abort wrote the last image a second time. Pre-existing; the new branch made it visible. Verified against a running broker on the local configuration: a colliding master file and a colliding data file are both refused by /start, /wait_until_running and /wait_till_done with the writer's own message, and the log shows the receiver was never started for either; a cancelled collection still answers 200. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016WmryXe8ASbNi632sUMfsa	2026-08-27 12:20:29 +02:00
leonarski_fandClaude Opus 5	f7cb701f43	rugnux: let --model settle the indexing of the reflections it writes ... ValidateAgainstModel was called after WriteReflections, so the two relabelings it makes - the change of hand where the data were merged in the model's enantiomorph, and the alternative indexing it picks by R-free where no reference MTZ had already fixed it - reached the R-factors, the maps and _maps.mtz and nothing else. The .mtz/.cif/.hkl beside them kept whichever indexing the merge happened to land in, so a file whose maps came from a model could not be refined against that model without being reindexed first. Validation now runs before the reflection files are written and returns the operators it applied. AdoptModelFrame puts the merged reflections through them with a proper ASU reduction - ReindexReflections only relabels, which is all its scoring callers need - and the Bijvoet halves follow the Friedel sign of that reduction. The integrated observations are relabelled too, so --export-unmerged describes the same indexing as the merged files rather than a second one. change_of_hand_op is the inversion, so adopting a model's hand exchanges I(+) and I(-). On a tetragonal crystal whose enantiomorphic pair share their whole absence pattern, the search picks one of the two arbitrarily, and the exported anomalous differences were the wrong way round whenever it picked the other member from the model's. The written space group follows the hand, and so does the report that describes those files. The _process.h5 is deliberately left alone: its per-image reflections went to disk as they were integrated, and recording a group that did not match them would mis-merge on a later --mode scale. Nothing is lost - an enantiomorphic pair has the same Laue class and the same absences, so it merges identically either way. Serial stills could not use a model for this at all: each crystal is indexed in its own hand, so by the time there is a merge to fit a model to, the hands have already been averaged together, and reindexing the merged result as a whole cannot separate them again. ModelReferenceIntensities computes |F_model|^2 from the structure - Fcalc plus a flat solvent term at the standard constants, which are not fitted because there are no observations yet - and hands it to the per-image resolver that a reference MTZ already drove. It needs the cell and the group up front, which serial indexing wants anyway. Measured on a serial dataset in a merohedral trigonal group, at a fixed resolution limit so the shells match: CC1/2 better in 8 of 10 shells (79.7 to 82.5 overall), R_meas better in 9 of 10 (111.1 to 104.7), ISa 1.11 to 1.20, and R-free against a structure the merge never saw 0.393 to 0.375. The ambiguity probe now logs the runner-up R-free as well as the winner. On the same data the margin is 0.016 when the hands are mixed, where the two global indexings are tied because both are already inside every reflection, and 0.193 once they are not - the difference between a decision and a coin toss, which the old single number hid. The warning about an unresolved ambiguity no longer fires when a model will resolve it, and names the flags that would; and the summary line no longer offers the adopted group as its own alternative, which it did once --model had moved the run onto the member the search had listed as the alternative. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Vi1gV6Z45aZL5wLwe85Ksn	2026-08-26 20:04:02 +02:00
leonarski_fandClaude Opus 5	c29dd67b5f	Broker: stop reporting a failed calibration as a successful one ... Every calibration step signals failure by calling SetState and returning normally - none of them throws, so none reached the catch in CalibrateDetector. The unconditional SetState(Idle, "Calibration sequence done", Success) after the try block then overwrote all of them. /cancel during a JUNGFRAU pedestal therefore left the broker Idle and apparently ready to measure while holding a truncated G0 and default-constructed zeros for G1/G2, and every subsequent run was silently mis-converted with nothing in /status to show it. The genuine failures - "Pedestal not collected properly", "Mask not collected properly" - were hidden the same way. The steps now return whether they succeeded, and the sequence reports success only if they all did. A cancellation or a failure leaves the state Inactive with Error severity rather than Idle or Error: the calibration is undefined, so the detector has to be initialized again, which is what Inactive means everywhere else in the machine. The exception path joins them, since a throw mid-sequence leaves the calibration no better defined. Cancelled pedestals were already Inactive but carried Warning severity, which reads as an advisory. CalibrateJUNGFRAU now abandons the sequence at the first failure instead of collecting G1 and G2 on top of a G0 that was never measured - the cancel path already behaved that way - and ConfigureDetector is skipped when there is no calibration to operate with, a cancelled sequence having left the detector mid-abort. Both error paths that end an Initialize now notify the condition variable. The state has left Busy, but without the notification a client in /wait_until_running slept out its whole timeout - up to an hour, if it asked for one - before noticing a failure that had already happened. Separately, dataset_settings.space_group_number allowed 1..194 in the OpenAPI schema while the broker accepts 1..230, so every generated client's validate() rejected all 36 cubic space groups before the request left. The regenerated clients follow in the version bump. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Uwv9ScHtDH6g8tYgfSuApo	2026-08-26 16:58:03 +02:00
leonarski_fandClaude Opus 5	a6a715703f	Broker: report a failed asynchronous start instead of a timeout ... An acquisition started with async_start returns from /start before the measurement thread has run, so a failure there had no caller to raise it to. MeasurementThread stored it in start_exception, but only the synchronous branch of Start() ever read it. The ordinary-failure path - a writer refusing to overwrite an existing file, say - sets the state to Idle rather than Error, and Idle is what wait_until_running_post maps to 504 "timeout, need to restart". So the one case the async workflow exists to report came back as a timeout with an empty body, and the writer's message was dropped. /wait_till_done was worse: Idle is its success case, so it answered 200 for a run that never started. Only a critical detector fault, which leaves the state at Error, was reported at all. The wait functions now rethrow start_exception, so both endpoints produce the same 500 and the same message as a synchronous start. rethrow_exception does not consume the exception_ptr, so repeated calls all report the same failure. It is cleared by every entry point that begins new work - Start (before ImportDatasetSettings, which can throw), Initialize, Pedestal, LoadDetectorSettings, SetDarkMaskSettings - so a pending failure is never attributed to the operation after it. The synchronous branch no longer clears it, so a wait call made after a failed /start reports the failure rather than an apparent timeout. wait_until_running_post and wait_till_done_post drop their timeout == 0 special case, which called GetStatus() directly and so bypassed the rethrow: ?timeout=0 returned 200 from /wait_till_done where ?timeout=1 returned the error. wait_for evaluates the predicate before expiring, so the state reported is unchanged. JFJochReceiverService::Start clears the receiver status when the start fails. JFJochReceiver's constructor sets progress to 0 and a zeroed status before the throw, and nothing cleared it, so /status reported Idle with progress 0 - a stalled acquisition, to the frontend - and /statistics reported an all-zero run that never happened, until the next start overwrote it. Its catch widens to std::exception, so a non-JFJochException gets the cleanup and the logging it skipped before. Nothing else is left dirty by a refused start: the receiver keeps its null receiver and Idle state, PrepareAction only resets counters (the FPGA is armed in StartAction, in a thread launched after the start message goes out), and SendStartMessage precedes every std::async in the receiver constructor. The test starts four more times afterwards, one of them a complete acquisition with no re-initialisation in between. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Uwv9ScHtDH6g8tYgfSuApo	2026-08-26 16:13:53 +02:00
leonarski_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	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	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	a4228b9c1d	tests: follow REPORT_VERSION to 2 ... 80e10f51b added an anisotropy section to the result report and moved REPORT_VERSION from 1 to 2, but left ResultReportTest asserting 1, so the [Diagnostics] tag has been failing on this branch since that commit. The assertion is the point of the test - a consumer greps that key - so it follows the constant. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 20:57:37 +02:00
leonarski_fandClaude Opus 5	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_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	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	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	75f1c5f954	SHIM library improvements from the HDF Group	2026-05-08 11:39:51 +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	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_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
leonarski_f	4a852b4d6b	v1.0.0-rc.134 (#43) ... 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: Add better locking for detector object - should help, when detector initialization takes too long * jfjoch_writer: Enable writing single, integrated HDF5 file with both data and metadata * XDS plugin: Add generation of Jungfraujoch plugin for XDS * CI: Add tests with XDS and DIALS (`xia2.ssx`) Reviewed-on: #43	2026-04-09 13:30:47 +02:00
leonarski_f	6133da1377	v1.0.0-rc.133 ... 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: Use httplib for HTTP server instead of Pistache * jfjoch_broker: Drop OpenSSL support * jfjoch_broker: Base work for multi-lattice support in the future * Update dependencies to more recent versions (spdlog, HDF5, Catch2, httplib) Reviewed-on: #41	2026-03-26 20:50:33 +01:00
leonarski_f	166fcdb68f	v1.0.0-rc.131 (#39) ... 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.124. * jfjoch_broker: Fix bug in saving JUNGFRAU calibration (pedestal/pedestalRMS) * jfjoch_viewer: Fix calibration (pedestal) images being open flipped * jfjoch_process: Add space group detection (EXPERIMENTAL) Reviewed-on: #39	2026-03-07 11:34:04 +01:00
leonarski_f	928789a67c	v1.0.0-rc.130 (#37) ... 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.124. * jfjoch_broker: Rotation indexer has two retries if failes * jfjoch_broker: Rotation indexer handles small number of rotation images (like test shot) * jfjoch_broker: Integration calculates background mask based on R2 radius * jfjoch_process: HDF5 files are not saved by default Reviewed-on: #37	2026-03-06 14:38:56 +01:00
leonarski_f	64002f1e29	v1.0.0-rc.129 (#36) ... 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.124. * jfjoch_broker: Significant improvements in TCP image socket, as a viable alternative for ZeroMQ sockets (only a single port on broker side, dynamically change number of writers, acknowledgments for written files) * jfjoch_broker: Delta phi is calculated also for still data in Bragg prediction * jfjoch_broker: Image pusher statistics are accessible via the REST interface * jfjoch_writer: Supports TCP image socket and for these auto-forking option Reviewed-on: #36 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-03-05 22:13:12 +01:00
leonarski_f	3036b1d37f	v1.0.0-rc.128 (#35) ... 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.124. * jfjoch_broker: Handle properly reuse of image buffer locations * jfjoch_broker: Fix bug in counting idle slots * jfjoch_broker: Force obtuse angle for monoclinic cells * jfjoch_process: Change scaling refinement tolerance Reviewed-on: #35 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-03-03 22:24:44 +01:00
leonarski_f	f3e0a15d26	v1.0.0-rc.127 (#34) ... 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.124. * jfjoch_broker: Default EIGER readout time is 20 microseconds * jfjoch_broker: Multiple improvements regarding performance * jfjoch_broker: Image buffer allows to track frames in preparation and sending * jfjoch_broker: Dedicated thread for ZeroMQ transmission to better utilize the image buffer * jfjoch_broker: Experimental implementation of transmission with raw TCP/IP sockets * jfjoch_writer: Fixes regarding properly closing files in long data collections * jfjoch_process: Scale & merge has been significantly improved, but it is not yet integrated into mainstream code Reviewed-on: #34	2026-03-02 15:57:12 +01:00
leonarski_f	32b681e591	v1.0.0-rc.126 (#33) ... This is an UNSTABLE release. If things go wrong with analysis, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Fix bug for monoclinic space groups being wrongly refined when beta is much different from 90 deg. Reviewed-on: #33 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-02-19 07:01:38 +01:00
leonarski_f	1ab257af6c	v1.0.0-rc.125 (#32) ... This is an UNSTABLE release. This version adds scalign and merging. These are experimental at the moment, and should not be used for production analysis. If things go wrong with analysis, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Improve logic on switching on/off spot finding * jfjoch_broker: Increase maximum spot count for FFBIDX to 65536 * jfjoch_broker: Increase default maximum unit cell for FFT to 500 A (could have performance impact, TBD) * jfjoch_process: Add scalign and merging functionality - program is experimental at the moment and should not be used for production analysis * jfjoch_viewer: Display partiality and reciprocal Lorentz-polarization correction for each reflection * jfjoch_writer: Save more information about each reflection Reviewed-on: #32 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-02-18 16:17:21 +01:00
leonarski_f	07fe4dd3bb	v1.0.0-rc.124 (#31) ... This is an UNSTABLE release. This version significantly rewrites code to predict reflection position and integrate them, especially in case of rotation crystallography. If things go wrong with analysis, it is better to revert to 1.0.0-rc.123. * jfjoch_broker: Improve refection position prediction and Bragg integration code. * jfjoch_broker: Align with XDS way of calculating Lorentz correction and general notation. * jfjoch_writer: Fix saving mosaicity properly in HDF5 file. * jfjoch_viewer: Introduce high-dynamic range mode for images * jfjoch_viewer: Ctrl+mouse wheel has exponential change in foreground (+/-15%) * jfjoch_viewer: Zoom-in numbers have better readability Reviewed-on: #31 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-02-01 13:29:33 +01:00
leonarski_f	1c4dfd03e2	v1.0.0-rc.123 (#30) ... This is an UNSTABLE release. * jfjoch_broker: Use newer version of Google Ceres for (potential) CUDA 13 compatibility * jfjoch_broker: Improve performance of generating preview images, especially for large detectors (9M-16M) * jfjoch_viewer: Improve performance of displaying images, especially for large detectors (9M-16M) * jfjoch_viewer: Add more color schemes for better image readability * HDF5: Common mutex for reading and writing HDF5 if both operations were to happen in the same executable * HDF5: suppress warning if path (upstream group) doesn't exists when checking if leaf exists Reviewed-on: #30 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-01-30 13:43:09 +01:00
leonarski_f	e2b240356c	v1.0.0-rc.121 (#28) ... This is an UNSTABLE release. * jfjoch_broker: Report changes in the image buffer, so viewer doesn't reload constantly * jfjoch_viewer: Improve performance of loading images * jfjoch_viewer: Auto-throttle image loading in HTTP-sync / movie modes * jfjoch_viewer: Auto-foreground calculated with histogram * jfjoch_viewer: Fix rare segmentation fault Reviewed-on: #28 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-12-12 21:24:20 +01:00