303 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	89208697cb	common: reset the slot status before putting it back on the free list ... release() published the handle through ReleaseSlot and only then wrote status = InPreparation. ReleaseSlot makes the handle available to GetImageSlot immediately, and GetImageSlot hands back this very object without resetting it, so the receiver could observe the stale Sending status and throw "Trying to send image that is not in preparation", aborting the collection - or take the opposite interleaving and leak the slot. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-31 14:41:13 +02:00
leonarski_fandClaude Opus 5	0ca159449f	Bragg integration: integrate as far as the detector reaches, not to a fixed 1.0 A ... BraggIntegrationSettings::DMinLimit_A had a setter that nothing anywhere called, so it was always its 1.0 A default - in rugnux, the viewer and the broker alike, with no option or API field to change it. It feeds the predictor as high_res_A, which discards any reflection with |q| > 1/d_min, so integration simply stopped at 1.0 A however far the detector reached. Five of the 33 rotation test datasets have detectors reaching past it, down to 0.981 A. On one of them, run with no resolution limit, the shell table ended dead at 1.00 A with that shell still at CC1/2 55.6% and <I/sig> 3.4 - cut mid-shell rather than fading out. This branch had already made the sibling limits detector-driven (spot finding, scaling), so the pipeline was finding spots the detector could see and then refusing to integrate them. Make it a std::optional: unset means as far as the detector reaches, a value limits. The limit is only a bound on how far the lattice walk goes, never a second opinion on what is measurable - both predictors independently drop reflections that miss the detector (BraggPrediction.cpp, BraggPredictionRot.cpp) - which is what makes the detector's own reach the right default. rugnux gains --integration-high-resolution (0 = no limit, as for --spot-high-resolution); the derived per-axis prediction range resolves against the same number, so the two cannot drift. Full battery: 30/33 space groups, unchanged from before, 0 failures and the same three known mismatches; 22 of 32 crystals bit-identical and nothing worse than 5 observations in ~500k. The datasets that gain do so because their detector reached past 1.0 A - the effect is understated here because the harness caps each merge at the XDS resolution anyway. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-31 14:03:34 +02:00
leonarski_fandClaude Opus 5	b0e315e73c	Bragg prediction: derive the lattice walk from the cell, and expose it in the API ... Follow-up to making max_hkl a setting: it is now an optional, and unset means "take it from this crystal". The predictor keeps only |q| <= 1/d_min and h = a.q for the real-space axis a, so |h| <= a/d_min exactly - and likewise |k| <= b/d_min and |l| <= c/d_min. max(a,b,c)/d_min therefore bounds all three at once: nothing that could be predicted lies outside it, and nothing inside it is reached by a shorter axis. It applies to rotation and stills alike, both going through the one place the prediction settings are built. Offline (rugnux, viewer) the default is unset, so every crystal gets its own range; --max-hkl overrides it. Online the broker holds a concrete number, because the cost is the cube of it per image and a live acquisition should not have its frame rate decided by whichever sample is mounted: max_hkl joins bragg_integration_settings in the OpenAPI with a default of 100, so an omitted field arrives as that default (the generated model carries it) rather than as "derive it", and the frontend exposes it next to the integration model. Measured against a fixed 100 on six rotation crystals: three are bit-identical, two were being truncated and recover 419k and 5.8k observations with the high-shell CC1/2 going 15.1 -> 25.8% and 52.1 -> 55.3%, and the space group is unchanged 6/6. It reproduces a fixed 200 exactly, which is the bound being tight rather than merely safe. The sixth is worth recording: a 149/83/226 A cell derives 227, and because a single scalar has to cover the longest axis the cube is ~16x what a per-axis box would be - 22% wall clock, for a net 22 observations out of 364k (the per-frame 65536-reflection cap re-selects at the margin when more candidates are offered) and identical CC1/2, ISa and space group. Per-axis limits would remove that; the predictors already map a thread index to h, k and l separately. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-31 13:10:58 +02:00
leonarski_fandClaude Opus 5	a06c06931f	Bragg prediction: how far to walk the lattice is a setting, not a literal ... max_hkl was hardcoded to 100 at the one place production builds the prediction settings, so the only way to change it was to edit and rebuild - and it is not a constant of the method, it is a property of the cell. An axis is truncated once a/d_min exceeds it: 100 covers a 150 A axis at 1.5 A, but the same axis at 1.0 A, or a 250 A axis anywhere, loses its outermost reflections with nothing said. Move it into BraggIntegrationSettings next to the other prediction/integration parameters and add rugnux --max-hkl (1..511, default 100 - no behaviour change). Like the integration radii and the background trim it stays out of the OpenAPI, so the broker keeps the default it has today and live analysis cannot be handed a range that would not finish; the offline front end, which knows its cell, can ask for more. RugnuxCommandLine emits it when it is not the default. Measured on five rotation crystals at --max-hkl 200: two are bit-identical at no cost, and three were being truncated - one gains 419k observations (+17%) and takes its high-shell CC1/2 from 15.1% to 25.8% for +14% wall clock, the other two gain 12k and 5.8k observations with CC1/2 76.6->82.4% and 52.1->55.3% for +9% and +1%. ISa is unchanged throughout, and no frame overflowed the prediction buffer. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-31 12:00:45 +02:00
leonarski_fandClaude Opus 5	07607d3d47	Keep the online reflection cap where the transport can carry it ... Raising the per-image reflection limit to 65536 for offline reprocessing also raised the image-buffer headroom derived from it, and that headroom divides a FIXED total buffer - so every slot grew from compressed+4 MB to compressed+16.7 MB and the receiver's slot count, i.e. how much of a burst it can absorb, fell by about three. Online never needed the raised limit: measured on three serial stills datasets the worst frame predicts 1380 reflections, 14% of even the old cap. So split them, the same way the geometry refinement's stopping rule is split: online keeps the transport-sized 10000, offline gets the full 65536, and the buffer headroom derives from the online one. Both still come from BraggPrediction so the cap, the prediction and the headroom cannot drift apart. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 22:49:16 +02:00
leonarski_fandClaude Opus 5	ade61eea60	Rotation: predict without truncating, and keep the better of the two passes ... Digging into the selection logic showed the caps were not deciding the science - the two-pass geometry post-refinement was, and the caps only fed it randomness. Caps. The prediction buffer now grows to whatever a frame predicts instead of keeping an arbitrary subset of it, and the per-image reflection limit is raised to 65536, with the image-buffer transport headroom derived from the same constant so the two cannot drift. Measured: bit-identical output on five battery crystals, because a normal cell never approached the old limits - only a large cell (~2.8e6 A^3, ~30000-44000 predictions per frame) ever did. Pass-2 guard. The refined pass is normally the better answer, which is why it is the canonical output, but it was adopted whatever it produced. On that same crystal it merged more unique reflections than its own cell can hold - completeness "117%", which is arithmetically impossible - while the header- geometry pass sat at 92.6% and CC1/2 0.98. Compare the two and, when the refined pass is not credible, go back to the header geometry and re-run so the canonical files are the ones that are kept. Both bounds are set where only a failure reaches them. Together on that crystal: 111639 unique against XDS's 118730 (was 88000-99000 and different every run), CC1/2 98.0% (was 96.9-97.7%), ISa 8.54, and two runs now agree bit for bit. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 19:20:51 +02:00
leonarski_fandClaude Opus 5	a95aca382c	Remove dead code left behind by recent changes ... None of this has a reader: - ScalingSettings::scaling_regularize and its setter/getter - ScaleOnTheFlyResult::succesful (never set) and ::time_s (set, never read), with the timing that only fed the latter - JFJochImage::last_fit_viewport_ (written twice, read nowhere) and the comment claiming the retry uses it - the retry keys off initial_fit_done_ - JFJochDiffractionImage::ice_ring_width_Q_recipA, and a QtConcurrent include in a file that uses none - an unused gemmi::Op accumulator in the spindle-angle helper - <random> in Merge.{h,cpp}, from before the half-set split became a hash - an orphaned comment describing the Ceres B-factor residual deleted in 014e43a4c, and two trailing comments that had collided on one line Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 11:29:42 +02:00
leonarski_fandClaude Opus 5	9b55e44acd	Azimuthal integration: clamp a negative variance before the square root ... calc_std uses the cancellation-prone (sum2 - sum^2/n) form on float accumulators summed over millions of pixels, so a flat ring - true variance near zero - comes out negative as often as positive and GetStd() returns NaN. Both adaptive spot-finder ring accumulators already floor this at zero; this one did not, and 1a0774eed made sum2 correct, so the path is now actually exercised. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 10:56:06 +02:00
leonarski_fandClaude Opus 5	2ef8841983	Azimuthal integration: keep the low Q limit below the maximum ... Making the high limit optional removed the implicit upper bound on the low one (it used to follow from high <= maxQ and high > low), so --azim-min-q 50 with no maximum is accepted and ResolveHighQ then calls std::clamp with its lower bound above its upper bound, which is undefined. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 10:56:06 +02:00
leonarski_fandClaude Opus 5	009555bc49	Spot finding: a zero high-resolution limit means no limit here too ... Every other reader of spot_finding.high_resolution_limit spells "unset" as value_or(0) and compares, so 0 and nullopt are interchangeable - except in SpotAnalyze, which passed the 0 straight to ResolutionShells and threw "Resolution must be above zero" on every image. Reachable over the REST API, where 0 is the natural way to say "no limit" and the settings check lets it through; the rugnux CLI already maps 0 to unset before this point. While here, check that a limit that IS set is finite regardless of its sign - NaN fails the > 0 test and was skipping validation entirely. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 10:55:19 +02:00
leonarski_fandClaude Opus 5	0162afd324	Azimuthal integration: report the dimensions of the image the mapping covers ... The mapping took its width and height from the CONVERTED geometry unconditionally, while pixel_to_bin is sized per mode: converted when the geometry is transformed, raw module layout when it is not. In raw mode the two disagreed - 2068x2162 reported against a 1024x4096 map on a JF4M. Only the adaptive spot finders read those dimensions, and they read them for exactly the thing that breaks: the CPU finder derives npix = w*h and then indexes the image, pixel_to_bin and the resolution mask with it, so it walked ~277k pixels past the end of all three; the GPU finder stays in bounds but decodes the strong-pixel bit index with the wrong row stride and reports spots at wrong coordinates. Nothing combines raw geometry with adaptive detection today, so this was latent rather than live. Take them from GetXPixelsNum()/GetYPixelsNum(), which already follow the geometry mode. The converted path is unchanged - it is the same number there - and every internal use is inside SetupConvGeom, which only runs when the geometry is transformed. Covered by two tests: the mapping's dimensions must match pixel_to_bin in both modes, and the CPU adaptive finder must return a spot planted on a raw-geometry image at that raw pixel. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-29 09:31:58 +02:00
leonarski_fandClaude Opus 5	1a0774eed0	Azimuthal integration: clear sum2 along with sum and count ... Clear() reallocated sum and count but left sum2 as the constructor had sized it. Every caller reuses one profile across the images of a dataset (rugnux keeps one per worker, the viewer one per view), so the squares kept accumulating while the means restarted at zero: the per-image standard deviation written to /entry/azint and shown in the plots was meaningless from the second image on, and grew without bound over a run. The size mismatch was the sharper edge. Clearing to a mapping with a different bin count left sum2 shorter than sum, and GetStd() and operator+= then read past its end - reachable in the viewer by opening a dataset with a wider q range than the one before it. Both are covered by tests: the same frame twice with a Clear() in between has to give the same standard deviation, and a profile cleared to a wider mapping has to report the right value in a bin that only the wider mapping has. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-29 09:28:38 +02:00
leonarski_fandClaude Opus 5	f2b92e3f4d	rugnux: --search-min-zeta drops badly-measured observations from the symmetry search ... zeta is the sine of the angle between a reflection's rocking path and the spindle. Near 0 the reflection crosses the Ewald sphere almost tangentially, spends many frames in diffracting position and is measured worst. The de-novo space-group search asks how EQUAL an operator's paired intensities are, so its answer is dominated by whichever reflections are measured worst - and when the spindle lies in a lattice plane, an operator that permutes the two in-plane axes samples a different mixture of measurement qualities than one that only flips signs. That is not a fair comparison, and it can make a real symmetry operator look like a twin law. Measured on a thaumatin set mounted that way (its 4-fold is 88.9 deg from the spindle), the added operators' disagreement is 1.74x the parent's over pairs where both reflections have zeta < 0.85 and 1.003x - i.e. the symmetry is exact - over pairs where both are above it. The search consequently refuses the 422 promotion and merges the crystal in P222, while the same data forced to the right group give CC1/2 99.2% at multiplicity 10.7, matching XDS. With the option the de-novo pass ignores those observations (the final merge keeps everything - there completeness is the point): zeta cut observations ignored H ratio adopted 0 (off) - 1.47 P222 0.5 1620648 1.44 P222 0.7 3006013 1.34 P21212 0.85 4536724 promoted P4212 (correct point group) OFF BY DEFAULT, and it must stay off, because the same cut costs four other crystals their space group (P41212 -> P212121, I23 -> P2, I23 -> I222 twice): at 0.85 it discards 40-80% of all observations, which on a crystal whose geometry is not the problem simply starves the search. Two independent implementations - filtering the pairs that enter the statistic, and filtering the observations that enter the merge - trade exactly the same crystals, so this is a property of the cut and not of where it is applied. Verified bit-identical to the previous binary when off. The companion diagnostic is already there: the run now reports how close a symmetry axis lies to the spindle, which is the geometry that makes this option worth reaching for. Implementation note for anyone tempted by the cheaper route: excluding these observations from the ASU grouping alone does NOT work. The 3D combine selects partials on corr, not on their group, so their intensity still reaches the fulls and the merged intensities are unchanged - measured, the statistic did not move by 0.03 while 67% of observations were nominally excluded. Zeroing corr is what removes an observation from the combine, the merge and the error model alike. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-28 20:03:43 +02:00
leonarski_fandClaude Opus 5	16bf3408f0	Address code-review findings; make detection limits detector-driven ... One changeset, developed together in response to a review of this branch, so the files carry several of the changes at once. Full test suite passes (733 cases). Spot finding - Split ImageSpotFinder into Detect() (flag strong pixels - the expensive per-pixel pass) and ExtractSpots() (CCL + min/max-pix + resolution mask), with Run() = both. The per-image min-pix escalation now detects ONCE and repeats only the cheap extraction, instead of re-running the whole finder four times per frame as it did on the default path. It also keeps the winning attempt's spot list rather than re-extracting it, so the frame that is integrated is exactly the frame that was scored - which a GPU re-extract could not guarantee (float atomic ordering). - spot_finding_time_s no longer swallows indexing time, and indexing_time_s now sums every escalation call instead of reporting only the last. Detection limits follow the detector - The azimuthal-integration upper q and the spot-finding high-resolution limit are now std::optional, in the C++ structs AND in the OpenAPI schema, and resolve to the detector's own maximum (DiffractionExperiment::GetDetectorMaxQ_ recipA). Adaptive detection reads a pixel's ring from the azimuthal bins, so a pixel outside that q range could never be strong - the integration range silently bounded what detection could see, regardless of the requested resolution limit. Regenerated the C++ and TypeScript clients; the viewer and the web frontend each gained a "to detector edge" switch. Detection defaults are now per workflow (measured, not assumed) - Stills: adaptive detection, min-pix chosen per image, no resolution clipping. - Rotation: fixed-threshold finder, min-pix 2, 1.5 A limit. On a 33-crystal rotation battery, adaptive detection helped four hard crystals but deterministically broke three (a lost space group, a halved indexing rate, a collapsed merge), and the detector-edge limit cost indexing on a strong rotation set (100.0 -> 96.8%). Each is still overridable by its flag, and --no-adaptive-spots is new. Indexer seed escalation - Stop escalating once a seed's lattice explains >= 90% of the seed spots. Previously any frame with >= 80 spots always paid three indexer calls, online broker included. Merge-consistency filter - --min-image-cc gated on a per-image CC computed BEFORE the stills partiality post-refinement and never refreshed; the refiner now recomputes it, so the reported CC describes the data that are actually merged. - Replaced the per-call cc_mask argument with one MergeOnTheFly flag, so the merge, the error model and MergeStats can no longer disagree about which images are in (the --scale path merged unfiltered while its statistics were filtered). Per-image B-factor refinement (-B) removed - Measured on four serial-stills datasets: it is a no-op where the per-image fit is well conditioned and actively harmful where it is not (CC1/2 -8.1, R_meas +23.2 on the weakest large-cell set, whose fits hit their [-50, 200] bounds on 14-25% of images). It had also been silently DISCARDED since the partiality post-refinement landed - reported but not applied. Rather than fix and keep a knob with no demonstrated benefit, the flag and the whole image_scale_b_factor chain are gone: setting, scaling fit, message field, CBOR, HDF5 write and read-back, per-image plot, OpenAPI enum, viewer column and checkbox, docs. ScaleOnTheFly no longer needs Ceres at all - the fit is a linear IRLS. (The Wilson per-image b_factor is a different quantity and stays.) Stills partiality width now fits both of its components - sigma^2 = gamma0^2 + (gamma_e*d*)^2 instead of a purely angular gamma_e*d* with gamma0 pinned to 0. Fitted per crystal by least squares of dist_ewald^2 on d*^2. The angular-only width is fitted over a d*^2-dense population, so it was pinned by the high-resolution edge and collapsed at low d*: median partiality 0.008 beyond 13 A for reflections that were plainly recorded, 55% of them under the merge's partiality floor, and the survivors divided by those values - which inflated the merged low-resolution intensity scale 3.6x (~ +9 A^2 of apparent B). Measured on 5000 stills: the ramp flattens to 0.89x, no observation is dropped any more (701750 -> 716811), shell-mean CC1/2 and R-free improve slightly. Note CC1/2, R_meas, completeness and a B-refining R-free are all blind to that ramp, which is why it survived earlier validation; the cost is high-resolution R_meas (98.5 -> 101.9 shell-averaged). Removed dead code from add-then-remove churn - Prediction-time "still partiality" (unreachable: no setter), the phantom IndexingSettings::min_indexed_spot_fraction knob (getter, no setter - now the constant it always was), StillsPartialityRefine's caller-less Settings constructor and its reference to a long-gone env var, ProcessImage's unread bool return, an unused include, and a dead viewer overlay hook. Also - Viewer: the magnifier compared a QImage with itself, so its scene rect was set once ever and it could not pan into a larger dataset; the hover tail timer could fire after leaveEvent and resurrect the resolution readout outside the image. - update_version.sh regenerated the frontend lock file BEFORE bumping the version (every release shipped an off-by-one lock), and did git rm/git add on a path that has not existed since the client moved to src/client - with no set -e, both failed silently. - fpga/pcie_driver/postinstall.sh tested "[ ! occurrences > 0 ]", which is a redirect, not a test, so dkms add never ran. - Unit tests for the adaptive-threshold host functions, which had none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-27 09:07:00 +02:00
leonarski_fandClaude Opus 4.8	a8c1006c49	Choose min-pix-per-spot adaptively per image for serial-stills indexing ... For stills indexing the minimum-pixels-per-spot filter is now chosen per image instead of being fixed: the frame is indexed at min-pix 3/2/1 and the setting that maximises indexed-spot count weighted by indexed fraction (n_indexed^2 / n_total) is kept, then integrated once at that min-pix. The fraction factor keeps a smaller min-pix's extra spots only when the lattice actually explains them, so strong frames retain their real weak spots (extending resolution) while noise-flooded frames stay strict. The mode is selected by the presence of --min-pix-per-spot, now optional (SpotFindingSettings::min_pix_per_spot is std::optional<int64_t>): omit it for the adaptive per-image path, give a value to force a fixed min-pix. It applies only to the stills indexing path -- rotation indexing builds one global lattice and keeps a fixed min-pix, and the online receiver and the FPGA host path always carry a concrete value, so neither changes. IndexAndRefine::ProcessImage now returns whether the frame indexed, to drive the per-image selection. Exposed in the jfjoch_viewer spot-finding settings (adaptive-threshold and adaptive-min-pix checkboxes, each greying out the control it overrides); the broker uses neither. Validated on the full rotation regression battery (no regression) and the whole serial-stills target battery at full image count. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-26 18:31:35 +02:00
leonarski_fandClaude Opus 4.8	014e43a4c9	Remove non-helping stills merge/scaling knobs ... Trims three opt-in stills parameters that did not improve data quality on the external-reference (PDB R-free) battery and only added code: - --partiality-uncertainty: the (1-p)/p merge-sigma term was null on all four serial-stills datasets of the battery vs their reference structures (and neutral-to-harmful at higher coefficients); removed the flag, setting and CorrectedSigma term. - --stills-modulation: the detector-plane flat-field surface was net-negative on flooded data; removed the flag, setting and MergeOnTheFly::RefineModulation (the rotation modulation in RotationScaleMerge is unaffected). - --min-indexed-fraction: every value other than the 0.20 default collapsed CC1/2; removed the override flag/setter, keeping the fixed 0.20 acceptance floor. Default behaviour is unchanged (all three were off / at their default). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-25 17:40:48 +02:00
leonarski_fandClaude Opus 4.8	20bbcb1cd3	Remove --soft-weight and --local-snr spot-finder options ... Both were opt-in adaptive-spot refinements that did not help. Soft per-spot weighting was index-rate neutral across the battery (re-ranking only bites when spots exceed the max-spot cap, which weak serial data does not reach). The local-SNR gate was neutral on index rate and degraded merged CC1/2 on flooded XFEL data. Drops the flags, ApplyWeights/FilterByLocalSNR, the per-spot weight field, and the by-weight FilterSpotsByCount branch (now strongest-first only). --adaptive-spots itself is unchanged. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-25 17:31:35 +02:00
leonarski_fandClaude Opus 4.8	ca7cbe206a	Add opt-in local-SNR spot gate and acceptance-fraction knob (serial stills) ... Two opt-in tools for weak serial-stills tuning; both default-off, so the default pipeline is bit-identical (verified: a serial-stills reference run reproduces HEAD's 7.85% indexing rate exactly). --local-snr <sigma> (AdaptiveSpotFinderCPU::FilterByLocalSNR): after the loose per-ring adaptive threshold builds connected-component spots, drop any spot that does not stand this many sigmas above its OWN LOCAL background (robust median/MAD of a square annulus), not just the azimuthal ring mean. On structured-background (XFEL) frames the ring mean underestimates the local diffuse level in some sectors, so the ring threshold floods; a real Bragg peak still stands many local sigmas proud. Validated on XFEL stills to separate real peaks from flood at the pixel level (real median local-SNR ~70 vs flood ~2.6; SNR>=5 keeps ~99.8% of real peaks, ~14% of flood). GPU-portable (a per-spot local reduction). NOTE: on the current serial-stills battery it is index-rate/CC1/2 neutral -- the flood that survives as CC clusters overlaps weak-real spots, and only lattice-fit separates those -- but it is the correct tool for genuinely floody data (ice/jet/loosened detector) and the right substrate for the online FPGA path. --min-indexed-fraction <f>: exposes the previously hardcoded 0.20 minimum indexed-spot fraction (AnalyzeIndexing) as a per-run setting. Lowering it admits weaker/sparser crystals; on flooded XFEL data the extra lattices are spurious (pair with --min-image-cc to gate them), on clean synchrotron data there are no marginal frames so it is a no-op -- useful as a gating-experiment primitive. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-24 11:12:22 +02:00
leonarski_fandClaude Opus 4.8	7c5bedfd74	Add soft per-spot quality weighting for adaptive spot detection ... Add --soft-weight (implies --adaptive-spots): give every detected spot a continuous quality weight in (0,1] and keep the highest-weight spots rather than the brightest, so a deliberately loose detector self-cleans -- bright ice / salt / jet blobs and single-pixel noise no longer evict faint clean Bragg spots from the max-spots cut. The weight is a product of dimensionless gates (AdaptiveSpotFinderCPU::ApplyWeights, computed against the per-ring background the adaptive finder already builds): a logistic ramp in the spot's SNR and a soft size band (rises from one pixel, plateaus, falls for oversized ice/salt/streak blobs). It carries on DiffractionSpot -> SpotToSave and is consumed by FilterSpotsByCount, which ranks by {non-ice, weight, intensity} when requested and by intensity otherwise, so the classic and FPGA paths are unchanged. Honest result: on the serial-stills battery this is index-rate-NEUTRAL. The weighted ranking only changes the outcome when the spot count exceeds the max-spots cap and the weight disagrees with intensity in a way that affects indexing; the adaptive detectors already produce clean spot lists and the weak sets sit under the cap, so re-ranking is a wash there (and a wash, not a regression, on the one set that floods). Its intended benefit -- robustness to ice/jet-contaminated frames and to a loosened detector -- is not exercised by this battery; kept opt-in as the substrate for that. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-23 19:53:55 +02:00
leonarski_fandClaude Opus 4.8	1a2b0181a5	Add physical partiality post-refinement for stills (default on) ... Replace the frozen scalar-sigma stills partiality with a physical, refined model. Per crystal, refine an orientation tilt (dpsi_x, dpsi_y) against the running merge and recompute each reflection's partiality analytically from the refined geometry (angular Ewald-proximity model, sigma(d*) = gamma_e*d*), with the per-crystal scale G profiled out by the existing robust IRLS - no re-integration. A soft Gaussian prior on dpsi tames weak-data overfit while staying inert on strong data. The merge <-> refine loop iterates a few times. This is now the stills default via ScalingSettings::stills_partiality_refine (on). A single opt-out flag `--simple-stills` reverts to treating every reflection as a full (p=1, single pass). Retires the experimental `--still-partiality` flag. The viewer gains a "Partiality post-refinement (stills)" checkbox in Scaling settings. Validated (integrate-once / --scale): CC1/2 and R_meas both improve on three monochromatic serial-stills datasets (+2.8 / -10, +5.6 / -3.4, +2.1 / -4); neutral on a pink-beam DMM set (already-full reflections); R-free/R-work down vs a fixed model; competitive with CrystFEL partialator on matched frames. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-23 14:45:43 +02:00
leonarski_fandClaude Opus 4.8	cbc6a85157	Debias stills merge with expected-variance weighting ... The serial-stills merge (MergeOnTheFly::CorrectedSigma) weighted each observation by 1/sigma^2 using the observation's OWN sigma. Below ~1 photon the Poisson signal part of that sigma correlates with the observation's up/down fluctuation, so the inverse-variance mean is biased low: an up-fluctuated observation acquires a larger sigma and is over-downweighted. The rotation combine (RotationScaleMerge:: process_rawrun) already avoids this by rebuilding the signal variance at the pooled estimate; the stills path did not. Decompose each observation's variance into a background/read part (kept per-observation) and a Poisson signal part, and rebuild the signal part at the reflection's expected <I>. Bit-identical when an observation sits at its reflection mean; only weak-shell weights move. Now default on, so the stills path matches the rotation path; --no-expected-variance-merge restores the old observed-sigma weighting. Validated by paired refinement (phenix, 5 free-set seeds, byte-identical free flags across arms): R-free-neutral on strong lysozyme and lower R-free on weak serial-stills data checked against an independent deposited model (6/6 seeds). The CC1/2 dip on strong data reflects precision, not accuracy. Applies to both offline rugnux and the online broker stills merge. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-22 22:50:25 +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	c49bd2ac3b	v1.0.0-rc.152 (#62) ... * jfjoch_broker: Fix bounds for azimuthal integration for Q spacing (allow Q of 1e-5) * jfjoch_viewer: Adjust Q bounds for azimuthal integration * jfjoch_azint: Add tool to do quick azimuthal integration Reviewed-on: #62	2026-06-17 20:36:24 +02:00
leonarski_f	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	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	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
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	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	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