leonarski_f
538f3504d3
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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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Linux package repositories
For convenience, we are providing package repositories. With versions including and excluding CUDA linking.
We recommend to install Jungfraujoch viewer from nocuda repository and remaining packages from cuda12/cuda13 repository.
The repository name encodes two choices: the slsDetectorPackage version the packages
were built against (slsdet8 = 8.0.2, slsdet9 = 9.2.0 — it must match the detector firmware) and
whether CUDA is linked in. What ends up inside each package, and what it needs on the target
machine, is described in Release contents.
RHEL based systems
For RHEL systems we provide the following repositories:
| RHEL version | slsDetectorPackage | CUDA | Repository file |
|---|---|---|---|
| 8.x | 8.0.2 | 12.x | https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-cuda12.repo |
| 8.x | 9.2.0 | 12.x | https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet9-cuda12.repo |
| 8.x | 8.0.2 | - | https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-nocuda.repo |
| 9.x | 8.0.2 | 13.x | https://gitea.psi.ch/api/packages/mx/rpm/centos/el9/slsdet8-cuda13.repo |
| 9.x | 9.2.0 | 13.x | https://gitea.psi.ch/api/packages/mx/rpm/centos/el9/slsdet9-cuda13.repo |
| 9.x | 8.0.2 | - | https://gitea.psi.ch/api/packages/mx/rpm/centos/el9/slsdet8-nocuda.repo |
To install the repository, run:
dnf config-manager --add-repo https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-cuda12.repo
RPMs are signed by the Gitea package registry as they are uploaded. If your system cannot verify the
signature, set gpgcheck=0 in the repository file or install with --nogpgcheck.
We provide the following packages in the repository:
- jfjoch — broker, web frontend, FPGA and detector command-line tools
- jfjoch-driver-dkms — PCIe kernel-module source, built by DKMS
- jfjoch-writer — HDF5 writer service
- jfjoch-viewer — desktop viewer, the offline analysis tools and the XDS plugin
Ubuntu based systems
For Ubuntu systems, we also provide the following repositories:
sudo curl https://gitea.psi.ch/api/packages/mx/debian/repository.key -o /etc/apt/keyrings/gitea-mx.asc
echo "deb [signed-by=/etc/apt/keyrings/gitea-mx.asc] https://gitea.psi.ch/api/packages/mx/debian $distribution $component" | sudo tee -a /etc/apt/sources.list.d/gitea.list
sudo apt update
$distribution uses Ubuntu names jammy (22.04) and noble (24.04). $component can be set to cuda13 and nocuda.
Only slsDetectorPackage 8.0.2 is built for Ubuntu.
The same four packages as above are provided: jfjoch, jfjoch-driver-dkms, jfjoch-writer and
jfjoch-viewer. Up to 1.0.0-rc.160 the first of them was misnamed jfjoch-jfjoch; the current
package replaces it, so apt upgrade handles the rename.
Ubuntu packages are currently only going through a very limited testing.