13 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	f0cdb027e1	Ice: default the merge mask off, gate the radial background on smooth ice, and pick detection by geometry ... Three defaults, each settled by measurement rather than by argument. The arbiter throughout is structure-referenced - anomalous peak height where a crystal can carry it, and otherwise the agreement of the ice bands with a fixed external model against resolution-matched DECOY bands carrying no ice. The band-versus-decoy contrast is used because R-free here tracks completeness, and every one of these switches moves completeness. The damage is real and it localizes: over the rotation battery the ice bands' excess amplitude reaches +9.6% on a smooth-ice crystal and +35% on the worst, while a clean control sits at +0.6% (z +0.45). On the worst crystal, nine of the ten largest excess peaks in a q scan land on hexagonal ring positions. Turning ice handling off leaves the contrast unchanged and forcing it on a clean crystal does not create one, so it is the ice and not the machinery. MERGE-TIME RING MASK -> OFF. It deletes reflections, which no other program does by default - AIMLESS, DIALS, xia2, XDS and CrystFEL all keep ice-band reflections in the merge and exclude them only from the model fit; autoPROC is the sole exception. On the one battery crystal where the mask fires and an anomalous arbiter can score it, dropping the band moved the mean peak height at the known sites by -0.001 +- 0.018 sigma, 2% of the site height, while removing 1149 unique reflections whose mean I/sigma was 3.62 against the dataset's own 3.05 - better than average data - and costing 17 completeness points in that shell. It fires on 5 of 37 crystals, changes no space group, and those 5 disagree in sign: it clearly helps the two most heavily iced, is a wash on two and costs a third. So it stays as a switch, worth setting by hand on a badly iced crystal where it shows in the high shell, but it is not a default. RADIAL BACKGROUND -> AUTO, gated per image. The correction models the background as a function of radius alone, and that is exactly when it works. On a crystal with pure smooth powder ice it removes 43% of the bands' excess amplitude, with the improvement 7x larger inside the bands than outside; on a crystal whose ice is discrete crystallite spots - no smooth ring to model - the excess amplitude GREW by half; on clean data it is inert to four decimals. The two ice channels already separate those morphologies, so --background-radial takes on|off|auto and auto applies it to an image when that image's peak-excluded score reaches --ice-min-score. Auto never engages without such a score, because the plain profile carries the Bragg peaks and cannot support an absolute threshold. Per image rather than per run, and that was tested rather than assumed: the gate fires on 100% and 94% of frames on the two crystals that want it, and on 1.5% of frames - 32 blocks, 23 of them single frames - on the textured-ice crystal. A seam statistic against off + f*(on - off) is null on both mixed runs, every merge statistic is bracketed by the pure arms, and the textured crystal's auto arm lands on `off` rather than on `on`'s harm. A run-level gate would need the score before the pass that integrates, i.e. rotation-only plumbing, and buys nothing measurable. The kernel was already built unconditionally, so flipping the flag per image is free - except on the GPU, where the launches were gated on a construction-time n_rad. That is why the buffers are now allocated whenever the correction could run, and Run() decides per image. DETECTION -> the geometry's default when the file is silent: on for rotation, off for stills, with the command line and then the file taking precedence. A rotation sweep sits on the same rings for the whole run, so ice there is a coherent systematic and the presence gate keeps it inert on a clean crystal; a serial stills run has too few spots per image to spend any on flagging. The master file's key is kept as written rather than collapsed to a bool, so "the file said nothing" is distinguishable from "the file said no" - it used to fall silently to off, taking the exclusion from the scale fit with it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-06 19:06:30 +02:00
leonarski_fandClaude Opus 5	61a7c91b90	Ice: detect it on two channels, and only handle it when it is there ... The per-image ice score was read off the PLAIN azimuthal profile. That profile is a per-ring mean, so a few strong Bragg reflections landing in a ring's q bin lift it exactly as ice would. Measured over 37 rotation crystals, that did not merely add noise - it INVERTED the metric: the two highest-scoring crystals had no ice at all (4.23 and 4.06), while a clean control read 1.57. A decoy null - the identical statistic evaluated at q positions where hexagonal ice cannot be - reaches 1.51 at its 99th percentile and 2.70 at its maximum, so that metric cannot support any absolute threshold whatsoever. The adaptive spot finder already computes the right input for its own threshold: a sigma-clipped per-resolution-ring background, in the same bins. A powder ring is azimuthally smooth and survives the clip; Bragg peaks do not. On the clipped profile the clean population tightens to 1.00-1.22 and the crystals with confirmed ice sit at 2.08-2.37, against a decoy null that never exceeds 1.29. That channel is blind to one thing: ice in large crystallites diffracts as DISCRETE spots and leaves the radial profile flat. So a second channel counts found spots on the rings against the same q width of ice-free flanks beside them. The two barely overlap - the smooth-ice crystals read 2.1-2.4 / ~1.0 and the textured ones ~1.1 / 3.8-17.6, while a clean crystal reads 1.04 on both. Both are then used as a GATE (--ice-min-score 1.5, --ice-min-spot-ratio 2.0, both calibrated on the battery, 0 disables): the eleven fixed hexagonal bands cover 16-26 % of the unique reflections at typical resolutions whether or not the crystal has ice, so flagging, the exclusion from the scale fit and the merge-time CC1/2 ring mask are now all skipped when neither channel sees any. The gate is applied in the full pipeline and in --scale, which reads the stored per-image values back out of the _process.h5. Also fixes the merge-time mask's control: the shoulder now excludes reflections that are themselves on an ice ring. The rings are not evenly spaced - 1.947/1.916/1.882 A sit 0.05-0.06 apart in q - so for those three the [w,3w) shoulder landed squarely on the neighbours and the test compared ice against ice. Measured, that is the only thing this changes: it removes firings on those three rings and leaves every other firing's CC pair identical to three decimals. And the online ice half-width, which was 0.02 in the API against 0.03 offline, so the same data got a narrower band online than the measured ~0.06 ring FWHM justifies. Battery (37 rotation crystals, against the previous behaviour): space groups 34/37 in both and NO crystal's space group changes; 6 crystals gain unique reflections, 1 loses. Best of them gains 7082 unique reflections with R_meas 16.0 -> 14.3, CC1/2 95.9 -> 97.3 and ISa 13.7 -> 19.0; another goes R_meas 54.9 -> 42.9, CC1/2 84.0 -> 90.4, ISa 3.9 -> 5.5; a third reaches CC1/2 99.4 from 95.7 at an unchanged reflection count. The one crystal that loses reflections improves on both R_meas and CC1/2. Not done here: the ScanResult/API/plot-type/frontend/viewer layers for the new spot_count_ice_control (they need the OpenAPI regeneration). Message, CBOR, HDF5 write/read and the receiver plots are. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-06 16:17:23 +02:00
leonarski_fandClaude Opus 5	ccbc366e2f	reader: read the frame number back with the reflections ... The per-reflection frame number is written to the process file and always has been, but the reader's designated initialiser simply omitted it, so every reflection came back at frame zero. Nothing complained, because zero is a valid frame. It matters because the 3D combine splits a reflection's partials into rocking events by frame contiguity. With every observation claiming frame zero there are no gaps to split on, so a reflection's entire rotation range collapses into ONE event: measured on a rotation dataset, 216066 fulls against 216705 distinct reflections, where the pipeline finds 367416. Forty-two per cent of the observations disappear, the goniometer-frame absorption surface evaluates every observation at a single angle, and the radiation-damage estimate is computed over a run that appears to last no time at all. The reason this survived is that the damage flatters: fewer, better-agreeing observations per reflection give R_meas sixteen per cent lower, ISa thirty per cent higher and a slightly better CC1/2 than the real merge. Anyone re-scaling a stored file was reading numbers that looked better than the pipeline's while standing on less than two thirds of the data, and one radiation-damage figure that was pure artefact. Read it as mandatory rather than optional-with-default, like h/k/l and the intensities: a silent zero is precisely the failure being fixed, and every file this function can read carries the dataset. After the fix the combine reproduces the pipeline exactly. The normal path does not go through this reader and is byte-identical before and after. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-02 13:37:13 +02:00
leonarski_fandClaude Opus 5	953302a9eb	Spot plot: the resolution axis comes from the detector, not from 1.5 A ... Dropping the fixed spot-finding limit left the reader still generating the spot-vs-resolution plot over shells that stop at 1.5 A, so a stored file reopened in the viewer showed a plot truncated at exactly the limit that was removed - GenerateSpotPlot drops every spot outside its shells. Pass the detector's own maximum resolution, as SpotAnalyze already does. That value is 0 when the geometry gives no scattering angle at all (no distance or no wavelength), and ResolutionShells throws on a non-positive d_min, once per image. There is no resolution axis to plot against in that case, so skip the plot. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-31 11:51:22 +02:00
leonarski_fandClaude Opus 5	8dc7254624	reader: the stored images are int32, so say so ... b81c6f00b took the container depth from bit_depth_image in the file, which fixed 32-bit EIGER2 files but got the general case wrong: the reader converts every image to SIGNED int32 (PixelSigned(true) a few lines up), while bit_depth_image describes an unsigned container, and GetOverflow() combines the two. So a 16-bit file still capped at INT16_MAX rather than 65535, and an 8-bit file newly capped at 127 - flagging counts 127..254 as saturated, which drops the whole reflection at the integration accept gate. Declare 32 bits, matching what the reader actually hands out. The saturation cap then comes from the file's own saturation_value, which is what it is for, and the error value reported for a read dataset becomes INT32_MIN - the sentinel the reader really uses. A file whose bit_depth_image is not 8/16/32 also stops throwing on open. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 10:57:33 +02:00
leonarski_fandClaude Opus 5	b81c6f00b7	reader: take the stored image bit depth from the file, not the DECTRIS default ... DetectorSetup hardcodes bit_depth_image = 16 for every DECTRIS detector (DetectorSetup.cpp:78), and GetByteDepthImage() consults that BEFORE the depth the reader takes from the file - so a file storing 32-bit images had its overflow computed as a 16-bit one. With the reader also declaring the images signed, GetOverflow() returned INT16_MAX and GetSaturationLimit() became min(file value, 32767). Every count above 32767 was therefore marked saturated, and because the integration accept gate requires ALL inner pixels valid, the whole reflection was discarded. That silently removes the strongest reflections of a strong crystal - the low-resolution ones that anchor scaling - while the file itself declares saturation at 105000-133000. Measured on a lysozyme rotation set (200 frames), before -> after: saturated pixels per frame 0.815 -> 0.000 brightest accepted pixel 32738 -> 87633 mean per-frame maximum 26218 -> 37390 i.e. the ceiling was exactly INT16_MAX and nothing genuine reached it. Which datasets this touches depends on how bright they are: measured pixels above the old ceiling range from 0.0 per frame on some rotation sets to 6.1 on others, so the fix is a no-op on weak data and only ever adds reflections. Rotation battery, 33 crystals: no point group changed (30/33 before and after) and no run failed. Four crystals move on quality, in both directions - ISa 1.90 -> 2.40 and 3.29 -> 4.80 on two, 2.97 -> 1.85 and 20.83 -> 18.47 on two others; three of the four are the battery's known weak or run-to-run-unstable crystals. The one strong crystal that moves gains 136 observations out of 1.9 million and loses 2.4 ISa: the reflections restored are by construction the brightest ones, and they carry the systematic error that the strongest reflections always carry. That is a real cost, but it is the cost of MEASURING them rather than discarding them unseen, and a lower asymptotic I/sigma on data that are now complete is preferable to a flattering one on data that quietly are not. Only the offline file reader is affected; the online path builds its detector setup from configuration. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-28 17:49:14 +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	81dbf9a385	Fix empty spot-plot and resolution percentile in SpotAnalyze ... GenerateSpotPlot iterated msg.spots, but SpotAnalyze called it before assigning output.spots. In the online path the DataMessage is fresh per frame, so the plot was built from an empty list and spot_plot_intensity / spot_plot_count came out all zeros. Pass the finished spots vector explicitly instead of relying on the field being set: the live path passes the full pre-truncation list, the HDF5 read-back path passes message.spots. GetResolution scaled the 5th-percentile index by spots.size() (which includes ice-ring spots) while indexing the ice-filtered resolutions vector, biasing the estimate and reading out of bounds on ice-heavy frames. Index by resolutions.size() instead. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-21 09:53:33 +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	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	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