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Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	f6bfa54624	Space-group search: score operators on normalised intensities ... Symmetry operators were scored by Pearson correlation on raw merged intensities. Both members of a symmetry pair sit at the same |s|, so the resolution fall-off is variance the two arms share exactly, and it inflates the correlation of true and false operators alike. The clearest demonstration is the test this commit adds: a synthetic data set with no symmetry at all - a radial fall-off times an independent per- reflection factor - is assigned point group 432 by the shipped code, with all 23 rotations confirmed at 0.632 to 0.656. The existing suite passes identically before and after, because nothing covered this. The new case fails 64 of its 100 assertions on the old scoring and passes on the new. On real data the same effect had the gate leaking: on one cubic crystal three pseudo-symmetric operators scored 0.506 to 0.517, above the 0.5 bound, so they were confirmed and 432 had to be refused further downstream by the twin-law and systematic-b guards. Scored on E-squared they read 0.283 to 0.298 and exactly the eleven genuine rotations of 23 are confirmed. The normalisation has to be over the reflections the correlation actually pairs. Reusing the existing normalised array is worse than doing nothing: it is normalised over the set the absence tests use, whose surviving fraction is itself resolution-dependent, and the coupling to the resolution cut rises from 0.086 to 0.262 against a raw baseline of 0.086. Normalised over the paired set it falls to 0.023. The twin-law H statistic keeps its own vectors on raw intensities. It shares the pair arrays with the correlation, and normalising in place moves it by up to 12% against a bound whose window is 5.5% wide. Verified rather than assumed: two instrumented binaries print the same H to twelve significant figures while the correlation differs. min_operator_cc goes 0.5 to 0.30. Normalised correlations run lower, and the observed window on rugnux's own search merges is 0.298 to 0.351; 0.35 is too high, because one crystal's weakest genuine operator reads 0.351. The headroom between a crystal's weakest true operator and its own measured false -operator floor widens on 14 of 14 crystals, median 0.430 to 0.619, and the worst operational margin goes from 0.031 to 0.051. Battery, twice, against a baseline reproducible to zero: the space group is identical on all 38 crystals, per-shell merging is 0 better and 0 worse across all 380 shells, and the merged mmCIF is byte-identical on 38 of 38 - on the 12 crystals whose integration radius now adapts as well as the 25 that do not. The arm is live rather than inert: all 313 operator correlations move while every pair count and every H value stays bit-identical, and on one cubic crystal three operators that raw intensities confirmed are rejected, with the space group unchanged. Following Padilla and Yeates (2003) Acta Cryst. D59, 1124-1130 for why a resolution-normalised statistic is the right one for a symmetry test. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-26 00:27:13 +02:00
leonarski_fandClaude Opus 5	80e10f51b3	rugnux: measure and report diffraction anisotropy ... rugnux now says whether a dataset's fall-off is direction-dependent, and by how much. It corrects nothing and truncates nothing: no intensity is changed, no reflection is dropped on a directional criterion, and the written files do not depend on direction at all. Two quantities, because they are not the same thing. The anisotropic deltaB is the range of the principal components of the anisotropy tensor - a rate of fall-off. The diffraction limit along each principal direction is where <I/sigma(I)> in a 20 degree cone falls through 2 - where signal actually runs out. One battery case has only 0.28 A between its directional limits and a 58x ratio in cone <I/sigma>, so reporting either alone would miss it. The tensor is a Laue-constrained deviatoric ADP tensor fitted on INTENSITIES with no positivity cut, by weighted Gauss-Newton over 12 shells x 60 directions with a free constant per shell. Fitting amplitudes after a positivity cut, which is what xtriage and ctruncate do, destroys about 40% of the measured anisotropy - the cut keeps only the positive noise excursions in whichever direction has died, and that is the direction carrying the signal. Against the same 38 merged files rugnux reads 1.24x xtriage's eigenvalue spread and 1.61x ctruncate's; on strong near-isotropic data all three agree to a few percent, and they diverge exactly where a direction has died. The verdict is gated three ways - not detected, detected, or cannot determine - against the dataset's own systematic floor, measured in the tensor directions its Laue symmetry forbids. The floor cannot be measured on merged reflections, which have exact Laue symmetry by construction, so the floor is taken from the unmerged observations and the verdict is "cannot determine" without them. Triclinic has no forbidden subspace and always returns cannot determine. A cubic crystal returns exactly zero, because that is its symmetry and not a measurement. A second axis reports the resolution signature: a genuine Debye-Waller fall-off is linear through the origin in s^2, and a deficit that is flat is something else. Magnitude alone had promoted a crystal that is 68% not a Debye-Waller B into the top five of this battery; it now reads not detected with the caution attached. Following Sheriff & Hendrickson (1987) Acta Cryst. A43, 118-121 for the tensor and Popov & Bourenkov (2003) Acta Cryst. D59, 1145-1153 for the estimator. The directional limits are written as jfjoch_ local mmCIF items rather than _reflns.pdbx_aniso_diffraction_limit_*, whose dictionary definition is explicitly the ellipsoid fitted to a diffraction cut-off surface - a construction rugnux does not perform. The generic anisotropic B tensor items are written. Changes no existing number; only REPORT_VERSION moves, 1 to 2. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 19:13:16 +02:00
leonarski_fandjungfrau	4dc2534dbf	v1.0.0.rc-162 (#72) ... **Files written by Jungfraujoch now import correctly in DIALS, XDS and pyFAI.** A tilted detector, a grid scan, a still recorded at a goniometer position, and saturated or unreadable pixels were each described in a way that a third-party program acted on wrongly. If you process Jungfraujoch data outside Jungfraujoch, prefer this release to any earlier one. * HDF5: the detector tilt (`rot1`/`rot2`/`rot3`) is exported correctly in the NXmx transformation chain; untilted geometries are unaffected. * HDF5: a still recorded at a goniometer position is no longer read back as a single image, and a grid scan records a stationary spindle so a program that requires a rotation axis can open it. * HDF5: the sample transformation chain is written in mounting order, with a Smargon head position told apart from the spindle, one entry per image, `module_offset` as a float unit vector, and `offset_units` on every offset. * HDF5: saturated, underloaded and unreadable pixels are described so a downstream program masks them - `saturation_value`, `underload_value`, `error_value` and `bit_depth_readout` are written correctly, and a data file missing next to a VDS master reads as the error marker rather than as zero counts. * HDF5: the rotation axis is read back under whatever name it carries, and `mirror_y` records whether the assembled image is mirrored in Y relative to the detector's raw readout. * A grid scan and a goniometer axis can both be set; they are no longer alternatives. * `images_per_file` is chosen from the acquisition when it is not given: a rotation sweep of at most 20000 images goes into a single data file, a grid scan splits on whole fast-axis rows, and stills and serial keep 1000. * The writer refuses a stream whose start message declares a different pixel format than its images carry, and a DECTRIS detector sending signed images is no longer declared unsigned. * The image stream can carry the sample transformation chain (`transformations`, in the END message); a producer that does not send it gets the same chain built by the writer. * rugnux: fixing the space group with `-S` no longer prevents the lattice from being found - a lattice indexed in a different setting is reindexed into that group's own setting, and a run whose crystal does not have that group's lattice stops and names the cell it indexed as, rather than reporting statistics that cannot describe it. * rugnux: the per-image resolution estimate now predicts the resolution the merged data reach rather than the highest-resolution spot found, and is reported as `SPOT_RESOLUTION_ESTIMATE`. * rugnux: two runs of the same command on the same images produce the same merged intensities; the azimuthal profile written alongside them is not yet reproducible in the same way. * rugnux: the offline lattice refinement is bounded by iterations rather than by a wall clock, so a loaded machine can no longer refine to a different lattice; a live acquisition keeps its real-time bound. * rugnux: the detector-frame modulation correction is fitted on a grid spanning the detector, so whether it is applied no longer depends on how far integration reached. * rugnux: the geometry pre-pass no longer writes `<prefix>_01.mtz`, `_01.cif`, `_01.hkl` and `_01_image.dat`; the refined second pass writes those files under `<prefix>`, and that is the result to use. * rugnux: `_process.h5` describes the pixel format of the images it links to, and is written on a thread of its own. * rugnux: the detector geometry is also logged in XDS's convention (`ORGX`/`ORGY`, detector axis vectors, rotation axis), so it can be compared with an XDS refinement. * rugnux: an image integrated in pyFAI through the `.poni` file written by `--mode calibration` comes out with the correct azimuth, and the file declares pyFAI's `orientation`, which needs pyFAI 2024.01 or newer. Radial integration is unchanged. * rugnux: a rotation run is substantially faster throughout - beam-stop detection, first-pass indexing, geometry refinement, integration, scaling and merging - and observations outside the scaling resolution range are dropped as they are ingested. The refined geometry, the space group chosen and the merged statistics are unchanged. * Faster spot finding and indexing, on the broker as well as in rugnux; the spots found and the lattices indexed are unchanged. * A run reserves substantially less GPU memory: nothing is allocated for buffers that are never read, and a worker builds only the engines it uses. * rugnux: with `-N` left at its default the per-image loop of `--mode mx` uses at most 16 workers per GPU, rather than one per hardware thread; an explicit `-N` is obeyed as given. * CUDA 12 builds now contain device code for Volta, so the RHEL 8 packages and the portable Linux `.tgz` run on a V100; the CUDA 13 artefacts (RHEL 9, Ubuntu, Windows) remain Turing and newer. * The build resolves a single Eigen for the whole project, and refuses to configure if Ceres picks up a different one; a build that mixed two Eigen versions was undefined behaviour and crashed at -O2. * Documentation: a security page, and the supported GPU generations and minimum NVIDIA driver version of every released artefact. **Breaking change to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.162, `frontend/src/client`): * `dataset_settings.images_per_file` is no longer `default: 1000` and no longer accepts `0`; it is optional, and its minimum is 1. A client sending `0` (previously "one file for the whole run") is now rejected - omit the field instead, which for a rotation sweep gives the same single file. * `file_writer_format` now defaults to `NXmxVDS`, matching the server's own default and the layout recommended for DIALS, XDS and CrystFEL. A generated client that fills in schema defaults and does not set the format explicitly will write VDS masters where it previously wrote legacy ones; set `NXmxLegacy` explicitly to keep them. --------- Co-authored-by: jungfrau <jungfrau@mx-aare-test.psi.ch> Reviewed-on: #72 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-08-25 08:21:39 +02:00
leonarski_f	538f3504d3	v1.0.0.rc-161 (#71) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * **rugnux: significantly better quality of results, and faster.** A large rework of integration, scaling, merging, geometry refinement and space-group determination, together with measurements the program previously made no attempt at - the direct beam before indexing, the beam stop, the goniometer rotation scale, and the stretches of a sweep the crystal did not deliver. A rotation dataset typically gains observations at better <I/sigma> and R_meas, and every `mx` and `scale` run writes a `<prefix>_report.txt` results report modelled on XDS's `CORRECT.LP`. Many defaults moved with it: spot detection is self-calibrating, beam-stop detection and rotation geometry post-refinement are on, resolution limits default to as far as the detector reaches, and ice-ring handling engages only where the crystal is measured to have ice. * **jfjoch_viewer:** the beam-stop shadow, the detector calibration and the beam-centre measurement are reachable from "Analyze dataset"; the settings panel reports how the sample moved and how polarized the beam was; image rendering and interaction are faster. * **Performance:** bitshuffle+LZ4 images are decoded on the GPU rather than on the host, with the bitshuffle inverse fused into preprocessing so the decompressed frame is never held in device memory. * **Broker, writer, packaging and build:** image-slot lifetime and locking fixes, per-image datasets sized by the images actually written, the Debian/Ubuntu broker package renamed to `jfjoch`, and `image_analysis` compiling under MSVC again. **Breaking change to the rugnux command line:** * `--azint-only` and `--scale` are **removed**, replaced by `--mode azint` and `--mode scale`; the full pipeline is `--mode mx` and remains the default. A script passing the old flags now fails with the list of valid modes rather than silently running the wrong one. * `-t`/`--stride` is **refused on rotation data**: skipping frames cuts every reflection's rocking curve, so the combined fulls and their partiality would be measured over frames the sweep never recorded. Select a contiguous range with `-s`/`-e` instead. `--mode azint` and `--force-still` still take a stride. **Breaking changes to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.161, `frontend/src/client`) or read the affected fields as optional: * `image_scale_b` is removed from the `plot_type` enum, so a client requesting that plot now gets an error rather than a curve. * `azim_int_settings.high_q_recipA`, `spot_finding_settings.high_resolution_limit` and `spot_finding_settings.low_resolution_limit` are no longer `required`. All three mean "no limit at that end" when unset and are omitted from the response instead of carrying a placeholder value, which raises in a client generated from an rc.160-or-earlier spec. A value of 0 is still accepted and means the same thing. **Breaking changes to the stored formats** - a consumer reading these fields must treat them as optional: * The per-image image-scale B factor is no longer computed, so `/entry/MX/imageScaleBFactor` is absent from newly written HDF5 files and the corresponding key is absent from the CBOR DataMessage and END blocks. Files written by rc.160 and earlier still contain it and still open; nothing in the pipeline reads it any more. * `_reflns.jfjoch_diffrn_ISa` now carries the whole-range `1/sqrt(a*b)` that XDS's ISa denotes, and the error-model `a` and `b` are reported in XDS's convention; the strong-reflection asymptote moves to `_reflns.jfjoch_diffrn_ISa_asymptotic`. **A file written by an earlier version carries the asymptote under the plain `ISa` name.** Reviewed-on: #71 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-08-13 17:03:10 +02:00
leonarski_f	1c4dfd03e2	v1.0.0-rc.123 (#30) ... This is an UNSTABLE release. * jfjoch_broker: Use newer version of Google Ceres for (potential) CUDA 13 compatibility * jfjoch_broker: Improve performance of generating preview images, especially for large detectors (9M-16M) * jfjoch_viewer: Improve performance of displaying images, especially for large detectors (9M-16M) * jfjoch_viewer: Add more color schemes for better image readability * HDF5: Common mutex for reading and writing HDF5 if both operations were to happen in the same executable * HDF5: suppress warning if path (upstream group) doesn't exists when checking if leaf exists Reviewed-on: #30 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-01-30 13:43:09 +01:00
leonarski_f	06c5b9cf7f	1.0.0-rc.65	2025-07-16 20:19:48 +02:00
leonarski_f	28d224afab	version 1.0.0-rc.25	2024-11-22 21:25:20 +01:00