20 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	e7be5447d3	receiver: stop copying every frame back from the device on the Lite path ... The Lite workflow built its analysis with the fused GPU engine disabled, which is also what decides whether the preprocessed image is copied device-to-host after every frame. So on a machine with a GPU the online path was moving the whole image back - 72 MB on a large detector, every frame, per worker - for a host reader that does not exist on that path. It was left off deliberately when the fused engine was added, to keep the online path unchanged in that commit, and never revisited. Nothing depends on it: the FPGA workflow uses a different analysis class, and strong-pixel values are read through a device gather rather than from the host image. Turning it on changes no result, and cannot: adaptive detection is unreachable online, because the REST schema exposes no way to enable it, so the classic GPU finder runs either way. Measured anyway, both engines on the same frames across five datasets including very weak ones: 2400 frames, 638260 spots, not one difference - identical lists, identical indexing rate, identical merge statistics to every printed digit. On a large detector with eight workers the median per-image cost falls from 94 to 59 ms and preprocessing from 21 to 6 ms; throughput rises from about 48 to 55 Hz. No percentile regresses, which is what matters for a service - the ninetieth improves from 128 to 74 ms and the tail with it. Spot finding gets faster too, because the large copy no longer contends with the device gather. Correct two statements while here. The flag's comment and the data-analysis document both said the online receiver uses the CPU adaptive finder; online never runs an adaptive finder at all, and the copy the flag really controls was not mentioned. That copy would be better expressed as what it is - whether a host engine will read the image, which the constructor already knows - rather than inferred from which spot finder is wanted. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-02 15:16:18 +02:00
leonarski_fandClaude Opus 5	4bdb229fb8	spot_finding: find connected components on the GPU ... The spot finder flagged strong pixels on the device and then labelled them on the host, so every frame sent the packed bitmask back - 2.26 MB on a large detector - and the host walked all of it to recover a few hundred pixels. Do the labelling on the device instead: compact the bitmask into a flat-index-sorted list, find each pixel's backward neighbours by binary search, union them lock-free with path halving, then label, accumulate and filter in one kernel. Only the spot list comes back, and only one stream synchronisation per frame. The gain in the ordinary case is modest - about a quarter off per-image spot finding - because the host algorithm is genuinely fast on a normal frame. What justifies it is the frame that is not ordinary. The host labels a sorted sparse list through a window spanning two detector lines, so its cost is quadratic in how many strong pixels share a line. A lit band of detector rows - a hot module, a panel edge - costs 33 ms at two rows and 377 ms at fifteen, all of it under the pixel cap that was supposed to bound this, and none of it maskable when the cause is a diffraction ring rather than a defect: a ring runs tangent to a row at its top and bottom, which is exactly the shape that hurts. The device version is flat at 0.05 to 0.64 ms across every geometry tried, so an online run no longer stalls a quarter of a second on an ice ring. Rejecting an over-cap frame is now free too, since the count is known before any pixel is written. Also label once and filter three times. The per-image minimum-pixel search runs the extraction at three settings, but that setting only decides which components are kept - it does not change the components - so the search itself need not be repeated. This helps the host path as much as the device one. The resolution mask moves to the device as a bit mask, uploaded when the limits change rather than per frame, since the compaction needs it there. Parity is asserted permanently rather than argued: five cases covering realistic frames, occupancy from a hundred pixels to past the cap, the pathological geometries including rings, the resolution mask, and a hundred-repeat determinism check - requiring the same partition, the same spot order, and identical counts. The centroid is a float sum and therefore order-dependent, so the device walks each component from its root in ascending order and fuses its multiply-add the way the host's does; note that whether the host fuses at all depends on the architecture flags, so exact centroid equality is asserted where the compiler fuses and a two-ulp bound otherwise. Making those accumulators integer would remove that dependence entirely and is worth doing separately. Regression set: all 37 crystals identical to the last printed digit. Unit suite passes with the new cases. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-02 13:34:43 +02:00
leonarski_fandClaude Opus 5	1a1e05ad14	spot_finding: run the same two passes on the CPU as on the GPU ... ImageSpotFinderGPU::Detect launches its kernel twice, feeding the first pass's strong-pixel bitmap back in so the second recomputes each local background with those pixels excluded and keeps them strong. The CPU finder ran a single pass, so the two returned different spot lists for the same frame and a dataset processed without a GPU did not match one processed with it. It matters for any spot wide enough to reach into its own 31x31 background box: the spot inflates the mean and variance it is then tested against, so its outer pixels fail the SNR test. On the test image added here - a 5x5 core at 300 counts with a one-pixel ring at 25 - a single pass returns the 25-pixel core and 7500 counts where two passes return the full 49 pixels and 8100. pxl_val also becomes int64_t, matching the GPU's pixel_result signature. It was int32_t, so pxl_val * pxl_val overflowed above 46341 counts even though the surrounding sums were already 64-bit. The new parity test compares PixelCount and Count, not just the centroid, which does not move for a symmetric spot whether or not the ring was picked up; it was confirmed to fail against the old single-pass CPU. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-31 15:37:22 +02:00
leonarski_fandClaude Opus 5	a3feb1271c	docs: CPU_DATA_ANALYSIS describes the algorithms, not their history ... The document had accumulated development narrative: what was tried and rejected, which datasets a change rescued or cost, measured percentages from test batteries. That belongs in commit messages and reports, not in a reference description of the pipeline - it dates quickly, and a reader looking up what an algorithm does has to sort it out from how it came to be. Removed throughout, keeping the algorithmic content and the design reasoning that explains a choice on principle: * 3.2 the whole paragraph justifying the rotation spot-finding limit from battery measurements, and the CPU-vs-GPU per-frame timings; * 3.3 "a significance/z-score was considered but is uninformative"; * 7.4 / 7.5 the comparisons to a robust loss and to joint refinement as approaches that had failed; * 9.2 the R_meas / CC1/2 outcomes attributed to the trimmed-mean background; * 9.3 "per-detector-region and crystal-anisotropy profiles were evaluated and add nothing"; * 10.2 the stills tilt "succeeds where a freely-fitted width collapses"; * 10.5 the CC_anom argument, trimmed to why the statistic behaves as it does; * 10.6 the survey of per-frame correlation medians across datasets; * 13 the space-group bullet, restructured into the three gates it actually applies, dropping the dataset anecdotes; * 14.2 the free-form per-shell rescale, stated as a design choice rather than an experiment. Section 13's space-group text was one 20-line paragraph; it is now a numbered list of the three tests, which is what the code does. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 10:11:33 +02:00
leonarski_fandClaude Opus 5	0f1851cf82	rugnux: drop the 1.5 A spot-finding limit on rotation data ... Rotation kept a 1.5 A high-resolution limit for spot finding on the strength of one indexing-rate measurement (100.0 -> 96.8% on a strong set). Measured properly, over the whole 33-crystal rotation battery, it does not earn its place: * no space-group decision changes - the same 30/33 agree with XDS, and the three that differ are the known pre-existing cases, unchanged; * 29 of 33 crystals are identical to the digit - same indexing rate, R_meas, CC1/2, ISa. The limit was doing nothing on the large majority; * where it does bite, the limit is the worse setting. The one crystal that loses appreciable indexing rate without it (99.50 -> 94.22%) comes back with lower R_meas (29.4 -> 28.1), higher high-resolution CC1/2 (27.9 -> 29.1) and higher ISa (5.77 -> 6.17). Another loses 0.4% of frames and gains 2.8 points of CC1/2_hi. Fewer frames indexed, better data from them; * runtime is unchanged (16m46s vs 17m32s over the battery). So the indexing-rate cost is real but does not carry through to the merged data, which is what the limit was protecting. Unset now means "as far as the detector reaches" for rotation as well as stills; --spot-high-resolution still sets a limit for weak, high-background data where the extra high-resolution spots are genuinely noise. This also removes the flag that distinguished "the user asked for no limit" from "the user said nothing" - with no rotation default left, both mean the same thing. While rewriting the comment block, corrects its neighbouring claim that rotation keeps the fixed-threshold finder; adaptive detection has been the default for both workflows since 6f4917dce. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-29 10:39:23 +02:00
leonarski_fandClaude Opus 5	323c76abde	docs: correct CPU_DATA_ANALYSIS against the code it describes ... Ten places where the document and the implementation had drifted apart. Each was checked against the source before rewriting: * 7.5 rotation post-refinement: it is TWO separate cross-validated steps (cell+axis from the angles, then distance+beam from the positions with the cell fixed), not one joint fit against the merged fulls; the held-out split is an hkl hash, not a frame split; the bounds are +-5% on distance and +-15 px on the beam, not "under ~1%"; and only the distance and beam centre reach pass 2, which re-indexes de novo. * 9.2 the trimmed-mean background: it is computed in the shared background pass, so it DOES apply to --integrator boxsum. Only the broadband sigma-clip is excluded. The section previously said both, contradicting itself two paragraphs apart. * 9.3 per-reflection profile rebuild, sub-pixel centring and radial elongation are gaussian-only; the empirical profile keeps the fixed per-shell grid and is accumulated on rounded predicted positions, not centroids. * 10.5 the asymptotic ISa and the b_ISa sigma floor are rotation-only; stills report 1/b and floor with the whole-range b. * 8.4 centering absences are applied only when the user fixes the space group - de novo, prediction runs in P so the search can confirm the centering from the intensities. * 10.6 per-batch relative-B cross-validates on ASU-group parity, not the frame parity the other surfaces use. * 13 the resolution cutoff sits one reported-shell width PAST the CC1/2 = 0.30 crossing, so data below 0.30 are kept. * 7.1 the orientation-only prior penalises all three components of the angle-axis vector. * 10.1 rlp is the RECIPROCAL Lorentz factor, L = 1/rlp. * 14.3 the model scaling is fitted over work and free reflections alike, so R-free is free of refinement, not of the scaling fit. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-29 09:41:32 +02:00
leonarski_fandClaude Opus 5	40acf1ffc4	rugnux: search the space group twice by default on rotation data ... --search-min-zeta now defaults to 0.85 for rotation, so the de-novo search runs on a merge of all the observations AND on a merge of only the well-measured ones, and keeps whichever found more symmetry. Previously it shipped off and the second opinion had to be asked for. Rotation battery, 33 crystals, NO flags beyond the resolution limit: fixed-threshold finder 30/33 - zero crystals differ from the single search adaptive finder 30/33 - the same three mismatches Both arms now agree crystal for crystal, which they have not done before. The last disagreement was a thaumatin set whose 4-fold sits 88.9 deg from the spindle: at defaults it now reads P42(1)2 (all-observation merge -> 222, Lorentz-filtered -> 422, higher taken) where it read P222. The classic arm is a strict no-op - zero differences against both the explicitly-flagged run and the run predating the dual search - so the default costs nothing where the geometry is not the problem, and 47.2 s against 47.8 s on the same crystal back to back. The default is safe to set because the two searches can only disagree by a LOST operator: discarding observations starves an operator correlation, it cannot invent one. That also makes the 0.85 itself uncritical - too aggressive a cut only means the second opinion contributes nothing and the full merge wins. --search-min-zeta 0 restores the single search. Docs: CHANGELOG gains a 1.0.0-rc.161 section covering the branch, and CPU_DATA_ANALYSIS records the four analysis changes of this work - the confidence-weighted per-image refinement, the collapsed per-frame scale guard, the opt-in per-image rejection, and the operator-disagreement criterion with the two-search rule. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-28 21:56:36 +02:00
leonarski_fandClaude Opus 5	6f4917dcee	rugnux: adaptive spot detection is the default for rotation data too ... It was held back because a 33-crystal rotation battery showed it breaking three crystals deterministically - a lost space group, a halved indexing rate and a collapsed merge. None of those causes turned out to be in detection. The extra spots adaptive finds are real. Measured per spot against a finder-neutral local background: 64% recur at the same position on the adjacent frame (chance rate 0.5%) with 2-frame rocking curves, and 0.00% would fail a conventional local SNR >= 4 test, median local SNR 34. What they include is genuine peaks belonging to no lattice the indexer found, and the damage they did scaled with their absolute COUNT (80.6 per frame against 36.8 for the fixed finder), not with their quality - which is why nothing aimed at judging individual spots ever worked. The three failures fell to fixes elsewhere: merge collapsed - a per-frame scale free to collapse toward zero amplified two junk frames by 546x (704098712, ec7a82613). Not a detection problem at all: the fixed-threshold finder trips the same bug on a different frame range. space group lost - the per-image geometry refinement was dragged 2.3-2.8 deg off by the weak-spot tail in an unweighted fit; weighting each spot by how strong it is FOR ITS RESOLUTION fixed it (ae126c3d5), and gained a point group for the fixed finder too. indexing halved - gone with the same two; that crystal is now better under adaptive (CC1/2 92.6 -> 95.9, high-shell 44.9 -> 56.4). Battery, 33 crystals, adaptive vs the fixed finder: exact space group matching XDS 26/33 vs 25/33 point group matching XDS 29/33 vs 30/33 ISa better on 6 crystals recovers a screw axis the other misses (P321 -> P3121) The one point group it loses is a tetragonal crystal where adaptive collects 2.4x the observations at better R_meas (21.4% vs 28.3%) and better ISa (4.58 vs 2.91), and forced to the right group gives CC1/2 99.2% at multiplicity 10.7 - matching XDS. Only the automatic symmetry call fails there, and six candidate causes have been measured and refuted (mixed indexing hands, off-crystal frames, a badly integrated minority, radiation damage, pseudo-tetragonality, uncorrected anisotropy). It is left as the subgroup, which is the recoverable direction: -S gives XDS-quality data from the same run, whereas the failures this unblocks were not recoverable. --no-adaptive-spots reverts to the fixed-threshold finder. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-28 11:59:37 +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	9fdeed282a	Add fused GPU adaptive spot finder (azint + spot finding in one pass) ... AdaptiveSpotFinderGPU does the per-resolution-ring reduction once on the GPU and drives both products from it: the azimuthal-integration profile (corrected space) and the self-calibrating adaptive spot-detection threshold (raw counts). This replaces the separate GPU azint pass and the host-side adaptive spot finder that runs on the GPU path today. On a ~4.5 MP detector it does both jobs in ~1 ms/frame versus ~40 ms for the CPU adaptive finder (~42x), with an identical spot list and azimuthal profile. The per-ring threshold math (Poisson tail + read-floored Gaussian, operating point from the false-pixels-per-frame knob) is factored into AdaptiveThreshold.h so the CPU and GPU finders share one source of truth and cannot drift. Wired opt-in via a MXAnalysisWithoutFPGA constructor flag, default on for the rugnux offline path and the interactive viewer, off for the online receiver (so the broker path is unchanged). When on, Analyze() skips the separate azint pass and lifts the profile from the fused engine. The viewer gains an "Adaptive threshold" checkbox that greys out the signal/noise and photon-count sliders (the adaptive finder uses neither). Dedicated tests exercise both products (spot-finding parity vs the CPU finder, azimuthal profile vs a standalone GPU azint) plus a speed benchmark. Validated end-to-end on lysozyme serial stills: fused == CPU-adaptive index rate and merge stats. Docs: new section 3.2 in docs/CPU_DATA_ANALYSIS.md. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-25 20:10:45 +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	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
leonarski_f	2ab9deb20b	v1.0.0-rc.123 (#40) ... Documentation update Reviewed-on: #40	2026-03-12 12:17:11 +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	061152279c	v1.0.0-rc.91	2025-10-20 20:43:44 +02:00
leonarski_f	c44a07aac2	v1.0.0-rc.90	2025-10-02 15:55:39 +02:00