leonarski_f
538f3504d3
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>
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Acknowledgements
Citation: F. Leonarski, M. Bruckner, C. Lopez-Cuenca, A. Mozzanica, H.-C. Stadler, Z. Matej, A. Castellane, B. Mesnet, J. Wojdyla, B. Schmitt and M. Wang "Jungfraujoch: hardware-accelerated data-acquisition system for kilohertz pixel-array X-ray detectors" (2023), J. Synchrotron Rad., 30, 227-234 doi:10.1107/S1600577522010268.
The project is supported by :
- Innosuisse via Innovation Project "NextGenDCU high data rate acquisition system for X-ray detectors in structural biology applications" (101.535.1 IP-ENG; Apr 2023 - Sep 2025).
- ETH Domain via Open Research Data Contribute project (Jan - Dec 2023)
- AMD University Program with donation of licenses of Ethernet IP cores and Vivado software
Decoding bitshuffle+LZ4 images on the GPU, rather than decompressing them on the host and uploading the result, follows Jon Wright (ESRF): "Experiences with GPU decompression for bitshuffle + LZ4 data", HDF5 User Group meeting (2021), and bslz4decoders. The CUDA kernels in Jungfraujoch are its own, but the approach is his.
Spot extraction groups strong pixels into spots with the sparse connected-component labelling of the ACTS traccc project: P. Gessinger, H. M. Gray, A. Krasznahorkay, C. Leggett, J. Niermann, A. Salzburger, S. N. Swatman and B. Yeo, "traccc: GPU track reconstruction library for HEP experiments" (2025), arXiv:2505.22822; traccc. The CPU spot extractor adapts its SparseCCL source, and the CUDA spot extractor follows the design of its GPU counterpart - a backward-neighbour graph over a sorted hit list, resolved by a parallel union-find. traccc is MPL-2.0; see THIRD_PARTY_NOTICES.md.
This software uses Viridis, Magma and Inferno colormaps from Matplotlib under its BSD-compatible license
Crystallographic methods adopted from other packages
The analysis pipeline reimplements methods first published, and in most cases first implemented, by other crystallographic software. The code below is Jungfraujoch's own; the methods are theirs, and are acknowledged here. Where a package's source was consulted this is said explicitly. None of these packages is linked or vendored, with the single exception of GEMMI (see THIRD_PARTY_NOTICES.md).
XDS — rotation geometry and notation, the reciprocal Lorentz and
partiality treatment, the maximum-likelihood mosaicity estimate, the MINPK criterion for rejecting
a reflection whose predicted profile is not cleanly its own, the intensity-based test for a
centred lattice, and the scaling correction surfaces indexed by image number and detector region. W. Kabsch, "XDS" (2010), Acta Cryst. D66, 125-132
doi:10.1107/S0907444909047337; W. Kabsch, "Integration,
scaling, space-group assignment and post-refinement" (2010), Acta Cryst. D66, 133-144
doi:10.1107/S0907444909047374.
Profile fitting with reweighted, de-biased variances is the Kabsch/Otwinowski iteration, from the second XDS paper above and from Z. Otwinowski and W. Minor, "Processing of X-ray diffraction data collected in oscillation mode" (1997), Methods Enzymol. 276, 307-326 doi:10.1016/S0076-6879(97)76066-X.
DIALS — the resolution cutoff from the CC1/2 fall-off, per-observation outlier rejection at merge, the scaling error model, and the treatment of a reflection whose background is contaminated. Its published behaviour, and in places its source, settled several choices here. G. Winter, D. G. Waterman, J. M. Parkhurst et al., "DIALS: implementation and evaluation of a new integration package" (2018), Acta Cryst. D74, 85-97 doi:10.1107/S2059798317017235; D. G. Waterman, G. Winter, R. J. Gildea et al., "Diffraction-geometry refinement in the DIALS framework" (2016), Acta Cryst. D72, 558-575 doi:10.1107/S2059798316002187; J. Beilsten-Edmands, G. Winter, R. Gildea et al., "Scaling diffraction data in the DIALS software package: algorithms and new approaches for multi-crystal scaling" (2020), Acta Cryst. D76, 385-399 doi:10.1107/S2059798320003198; J. M. Parkhurst, G. Winter, D. G. Waterman et al., "Robust background modelling in DIALS" (2016), J. Appl. Cryst. 49, 1912-1921 doi:10.1107/S1600576716013595.
POINTLESS (CCP4) — the space-group search. Stage A scores each candidate rotation operator by the correlation of I(h) with I(Rh); the screw-axis test scores a predicted-absent class against the rest of its own axial row rather than against a global mean or a fixed cut, and lets confidence fall away with the number of axial reflections instead of refusing below a count. P. Evans, "Scaling and assessment of data quality" (2006), Acta Cryst. D62, 72-82 doi:10.1107/S0907444905036693; P. R. Evans, "An introduction to data reduction: space-group determination, scaling and intensity statistics" (2011), Acta Cryst. D67, 282-292 doi:10.1107/S090744491003982X; P. R. Evans and G. N. Murshudov, "How good are my data and what is the resolution?" (2013), Acta Cryst. D69, 1204-1214 doi:10.1107/S0907444913000061; J. Agirre, M. Atanasova, H. Bagdonas et al., "The CCP4 suite: integrative software for macromolecular crystallography" (2023), Acta Cryst. D79, 449-461 doi:10.1107/S2059798323003595.
MOSFLM — the Rossmann FFT autoindexing algorithm and post-refinement practice, including which parameters are safe to refine per image and which must be refined over a wedge. A. G. W. Leslie and H. R. Powell, "Processing diffraction data with MOSFLM" (2007), in Evolving Methods for Macromolecular Crystallography, NATO Science Series II, vol. 245, 41-51 doi:10.1007/978-1-4020-6316-9_4; T. G. G. Battye, L. Kontogiannis, O. Johnson, H. R. Powell and A. G. W. Leslie, "iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM" (2011), Acta Cryst. D67, 271-281 doi:10.1107/S0907444910048675; H. R. Powell, T. G. G. Battye, L. Kontogiannis, O. Johnson and A. G. W. Leslie, "Integrating macromolecular X-ray diffraction data with the graphical user interface iMosflm" (2017), Nat. Protoc. 12, 1310-1325 doi:10.1038/nprot.2017.037.
CrystFEL — spot finding, the three-ring integration
region, the serial/stills processing model, and the per-frame indexing acceptance test
(indexing_peak_check() in peaks.c). T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass,
A. Barty and H. N. Chapman, "CrystFEL: a software suite for snapshot serial crystallography" (2012),
J. Appl. Cryst. 45, 335-341 doi:10.1107/S0021889812002312.
GEMMI — symmetry operations, unit-cell and
structure-factor machinery, and MTZ / XDS_ASCII I/O. Vendored in gemmi_gph/, so it also carries a
licence obligation. M. Wojdyr, "GEMMI: A library for structural biology" (2022), J. Open Source
Softw. 7, 4200 doi:10.21105/joss.04200.
Data-quality statistics follow the established conventions rather than any one program: R_meas and R_pim, CC1/2 and CC*, and the reporting of I/sigma(I). K. Diederichs and P. A. Karplus, "Improved R-factors for diffraction data analysis in macromolecular crystallography" (1997), Nat. Struct. Biol. 4, 269-275 doi:10.1038/nsb0497-269; P. A. Karplus and K. Diederichs, "Linking crystallographic model and data quality" (2012), Science 336, 1030-1033 doi:10.1126/science.1218231; K. Diederichs and P. A. Karplus, "Better models by discarding data?" (2013), Acta Cryst. D69, 1215-1222 doi:10.1107/S0907444913001121.
Uncertainty conventions follow the IUCr Commission on Crystallographic Nomenclature: D. Schwarzenbach, S. C. Abrahams, H. D. Flack et al., "Statistical descriptors in crystallography: Report of the IUCr Subcommittee on Statistical Descriptors" (1989), Acta Cryst. A45, 63-75 doi:10.1107/S0108767388009596; D. Schwarzenbach, S. C. Abrahams, H. D. Flack, E. Prince and A. J. C. Wilson, "Statistical descriptors in crystallography. II. Report of a Working Group on Expression of Uncertainty in Measurement" (1995), Acta Cryst. A51, 565-569 doi:10.1107/S0108767395002340.