18 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	0e23fd3ab9	Bragg integration: propagate the background-estimate uncertainty, add an opt-in radial background correction ... Two independent pieces in the same code path. The background-estimate variance was never propagated. A reflection's background comes from a finite ring of n_b pixels, so subtracting it adds var(B)/n_b per signal pixel - sqrt(1 + n_d/n_b) = 1.109 with the shipped stencil. Both engines omitted it, which is exactly the 1.11-1.19 gap measured between the off-ring scatter and the reported sigma. Three lines each; it affects every dataset, not only iced ones. The radial correction is new and OFF by default (--background-radial). The signal disk and the background ring are concentric, so for any background LINEAR in position <B>_ann == <B>_disk identically and a plane fit buys nothing; the leading error is the CURVATURE of the radial background, which on a sharp ice ring reaches +26 counts on a single reflection. Since every reflection uses the same stencil, that error is a fixed kernel over radial offset - one short dot product per reflection and no extra pixel reads. Validated on empty apertures before any C++: mean |bias| over 9 bands / 3 crystals 4.33 -> 0.79 counts with the scatter unchanged. Three things it cost a battery each to learn, all now in the code: - the radial curve must be accumulated from CLIPPED annulus pixels, inside the clip pass, or it carries neighbour tails and zingers (so it is inert under --integrator boxsum, which has no clip pass); - the GPU version was a 1.8x slowdown from atomicAdd contention on a small radial array - staged in shared memory per block it now costs nothing measurable; - it is battery-NEUTRAL as a default, because the reflections whose bias it fixes are the ones the ice handling already excludes. Hence off by default. CPU/GPU parity extended with two radial sections: 9002 assertions. Also fixes a latent French-Wilson quadrature collapse: j_max = I + 8 sigma on a fixed 400-point grid degenerates to a single cell once sigma >> 50 <I>, giving F = 0.1 sqrt(sigma) with sigmaF -> 0. Harmless today, but any sigma-inflation scheme detonates it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-06 15:44:13 +02:00
leonarski_fandClaude Opus 5	09fb8e0306	Bragg integration: clip the background ring high side instead of trimming it ... The r2..r3 background ring was averaged with a 10% SYMMETRIC trimmed mean. A symmetric trim is not a consistent estimator of the mean of a right-skewed (Poisson) sample: on a clean Poisson ring it sits ~0.1 ct/px BELOW the true mean at every level, and with ~50 signal pixels in the r1 disk that under-subtraction adds ~5 counts to every partial on every frame. Measured two independent ways on four rotation datasets - stored background_mean against a plain ring mean over the same pixels on reflection-free frames, and directly on apertures that provably hold no reflection. Empty-aperture pedestal, counts: plain mean -0.03..-0.20, 10% symmetric trim +5.05..+6.34, 4 sigma clip +0.02..+0.54. Replace it with a high-side-only sigma clip at mean + n*sqrt(mean), n = 4 for monochromatic data. It rejects the same one-sided contamination the trim was there for - better, in fact: a 40 px neighbour core at +100 ct shifts the trim by +10.1 ct/px, because a symmetric trim collapses once contamination exceeds ~10% of the ring, versus +0.009 ct/px at 4 sigma. False rejection on a clean ring is 0.04-0.39%. Broadband data keep their tuned 3 sigma clip unchanged. The trim stays reachable with --background-trim for back compatibility; setting either estimator clears the other, so they can never stack. --integrator boxsum does not take the clip (matching what the shipped clip already did), so it now uses the plain ring mean unless --background-trim is given. The intensities get measurably more accurate: per-shell agreement with an independent processing of the same images improves on 14 of 16 crystals (weighted -0.0347, outermost shell 12/4), the outermost-shell R_meas NUMERATOR - absolute scatter, not a denominator effect - falls 13.5% median on 16/5, and CC1/2 in the outer shell improves on 14/7. EXPECT <I/sigma> TO FALL AND EDGE R_meas TO RISE. Both are inflated by information-free counts, so both get worse when the bias is removed; neither is evidence against this change. That fingerprint is exactly how the trimmed mean was accepted in the first place. Known cost: over the 37-crystal rotation battery the de-novo space-group count goes 34 OK / 3 DIFF to 33 / 4. The single regression is a two-lattice crystal whose merge fails the absolute-sanity gate under either background (R_meas 63.5%, CC1/2 72.2%) and which carries an unresolved indexing ambiguity on the very operator being scored, so its operator CC is diluted by construction. No other crystal changes space group, and twin protection is not weakened - the H-ratio veto that refuses genuinely twinned crystals gets MORE decisive (1.63 -> 1.84, 2.83 -> 3.99). Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-05 18:03:11 +02:00
leonarski_fandClaude Opus 5	32ecc296b8	broker: bootstrap a concrete max_hkl, as the API and the docs already claim ... How far the predictor walks the lattice became a setting defaulting to "derive it from the refined cell", which is what is wanted offline. Online it is not: per-image prediction cost then depends on whichever crystal is mounted, and the cube (2n+1)^3 grows quickly. The broker was only ever handed a concrete value when a client sent a bragg_integration block, and none of the shipped configs has one, so the derived path was the normal deployment. Four places in the tree - the conversion, the predictor, the OpenAPI description and the changelog - already state that the broker keeps a fixed bootstrap. Make that true. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-03 14:14:09 +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	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_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	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	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	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	3c17ce3b0b	2509 integration development	2025-09-12 15:21:38 +02:00
leonarski_f	c67337cfe1	v1.0.0-rc.72	2025-09-08 20:28:59 +02:00
leonarski_f	0d1b388f4d	v1.0.0-rc.50	2025-06-20 09:52:26 +02:00