leonarski_f
749db470ca
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* rugnux now tells you whether a crystal diffracts anisotropically and how far it reaches in each direction, without a second program: a new `9. DIFFRACTION ANISOTROPY` section in `<prefix>_report.txt` and matching `_reflns.pdbx_aniso_B_tensor_*` / `_reflns.jfjoch_aniso_*` items in the merged mmCIF report the anisotropic deltaB, the diffraction limit along each principal direction, and a `NOT DETECTED` / `DETECTED` / `CANNOT DETERMINE` verdict measured against the data set's own systematic error. It is a description only - no intensity is corrected, no reflection is removed, and the merged data do not depend on direction.
* rugnux can hand its integrated observations to another scaling program: `--export-unmerged` writes `<prefix>_unmerged.mtz`, an unmerged MTZ readable by aimless, pointless, careless and `iotbx.merging_statistics`, in `--mode mx` and `--mode scale` alike. Each rotation reflection's partials are summed into one full; `--export-unmerged-partials` writes one row per image instead. Intensities carry the Lorentz-polarization factor and nothing else, since those programs scale the data themselves. Lattice-centring absences are not written; screw and glide absences are.
* rugnux integrates crystals with broad spots better - where it changes anything, per-shell mean I/sigma improves by up to 31% and R_meas by up to 24% - because on rotation data the integration signal radius is now taken from the crystal's own measured spot width instead of a fixed 4 px. `--adaptive-integration-radius=off` restores the fixed radius and an explicit `--integration-radius` still overrides both. The widened radius applies to the final integration pass only, and a pattern too dense for it is re-integrated at 4 px with a note in the log.
* rugnux discards fewer stills reflections for want of a background ring, improving per-shell R_meas over most of the signal-bearing range: the stills background ring now runs to 14 px instead of 12. The gain reverses in shells below a mean I/sigma of about 4.
* rugnux determines the space group with thresholds that mean the same thing on a weak crystal as on a strong one: symmetry operators are scored on resolution-normalised intensities (E squared) instead of raw merged intensities, and a reflection counts as genuinely present on its counting significance instead of on the merged I/sigma, which saturates at the merge's own ISa. The search resolution cut is no longer able to move the answer, and the twin-law H bound moves from 1.70 to 1.85, which stops one class of correct high-symmetry assignment being refused as twinning.
* rugnux says what the space-group search tested and what it could not: the twin-law disagreement H is printed for every operator together with the adopted point group's H ratio and its bound; alternatives that are not on the reported lattice are named with how their cell differs; and a lattice centring the data could not test - the crystal having been integrated on the primitive sub-cell, so the reflections it extinguishes were never measured - is marked `UNTESTED` and warned about where it is adopted, as coming from the lattice metric rather than from the intensities.
* rugnux `--mode scale` re-merges a `_process.h5` in the right symmetry without being told it: the file now records the space group on every run - a two-pass rotation run wrote none before, so re-merging defaulted to P1 - together with the change of basis under `/entry/MX/reindexMatrix` where the lattice was re-seated, and `--mode scale` also reports the Wilson B-factor estimate instead of `WILSON_B= nan`. A file written before this stops with a message naming the two cells and the override to use, instead of failing inside the merge. A third-party reader of a `_process.h5` must apply `reindexMatrix` where it is present.
* rugnux installs on its own, as a package called `rugnux` - `dnf install rugnux` or `apt install rugnux` - instead of arriving inside `jfjoch-viewer`. It pulls in none of the acquisition stack, so a machine that only processes data no longer has to carry the broker, the detector libraries or Qt to get it. Installing it over a `jfjoch-viewer` from rc.163 or earlier, which still owns `/usr/bin/rugnux`, upgrades cleanly rather than failing on the duplicate file.
* rugnux is also a standalone download, built for arm64 as well as x86_64: `rugnux-<version>-linux-{x86_64|aarch64}-cuda<major>.tgz` and `rugnux-<version>-win64-cuda<major>.zip` on the release page, for machines that are not managed by a package manager. The aarch64 build targets GH200 and DGX Spark, and is untested on hardware.
* Every portable Linux binary is now a single self-contained file: cuFFT is linked statically instead of being shipped beside the executable and found through an rpath, so `rugnux` and `jfjoch_viewer` need nothing but an NVIDIA driver, and only to use the GPU. The `.rpm`/`.deb` continue to take cuFFT from the distribution. The developer utilities `jfjoch_extract_hkl` and `jfjoch_recompress` are no longer packaged anywhere.
* Jungfraujoch needs six fewer shared libraries on the machine - libopenblas and libmetis, and libgfortran, libquadmath, libgomp and libz behind them - because the Ceres LAPACK, METIS and SuiteSparse back-ends are no longer built. Nothing in the code ever selected them, and results are unchanged.
* The PCIe driver DKMS package builds for the kernel it is being installed for instead of the running one, so a module built while a kernel update is being applied loads after the reboot.
* The PCIe driver builds on RHEL 9.5 and later, and on their CentOS Stream, Rocky and AlmaLinux equivalents, where the `vm_flags` kernel interface was backported into the 5.14 kernel.
* A data collection started with `async_start` that fails to start - a writer refusing to overwrite an existing file, for instance - is reported as an error by `/wait_until_running` and `/wait_till_done` instead of as a timeout and a successful collection respectively. The error message is the one the writer gave.
* A calibration that is cancelled or that fails to collect its pedestals is no longer reported as a successful one. The broker goes to `Inactive` with an error message and has to be initialized again, instead of sitting in `Idle` looking ready to measure while holding partial pedestals - data collected in that state was silently mis-converted.
* A failed `/initialize` is reported to `/wait_until_running` and `/wait_till_done` as soon as it happens, instead of when their timeout expires.
* `space_group_number` accepts space groups up to 230 in the API schema, so cubic space groups can be recorded. The broker always accepted them; the generated clients rejected them before the request was sent.
* The results report's `REPORT_VERSION` is 3, two sections having been added. Existing key names and table columns are unchanged.
* The merged statistics table has **9** resolution shells instead of 10, which is what XDS reports. The bins were already XDS's - equal steps in 1/d^2 between the lowest- and the highest-resolution reflection the merge kept - so at the same resolution limits the two tables now have the same shell boundaries and can be read row for row. `--resolution-shells` sets a different count.
* `rugnux --model` now settles the frame the merged reflections are written in, not only the frame the R-factors and the maps are computed in: the `.mtz`/`.cif`/`.hkl` come out in the model's indexing, and where the data were merged in the model's enantiomorph they take the model's hand and space group - which on anomalous data puts I(+) and I(-) the right way round. The indexing choice is logged with the winning R-free and the runner-up, so a decision made within noise is visible.
* `rugnux --model` can resolve the indexing ambiguity of a **serial stills** run, which a model could not do before: structure factors computed from the model become the per-image reference, the same role a reference MTZ plays. It needs the cell and space group up front (`-C` / `-S`). Without one or the other, a merohedral serial run still merges both hands together and says so.
* The rugnux documentation opens with a quick start - the default run, and runs with a reference MTZ, with a model, or with the space group and cell pinned - and explains the indexing ambiguity: what it costs on rotation and on serial data, and which of `-z` / `--model` resolves it in each case. The long reference pages now carry a table of contents.
Reviewed-on: #74
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
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Tools
Besides the main services (jfjoch_broker,
jfjoch_writer, jfjoch_viewer), the repository ships a
number of command-line tools. Each prints its own usage when run with -h or without arguments.
Data analysis
rugnux
Offline CLI tool that runs the full crystallographic analysis pipeline (spot finding, indexing,
integration, scaling/merging) on a stored HDF5 dataset, producing a _process.h5 file and, when
merging, reflection files. Merging is on by default (--no-merge disables it). --mode picks what a
run does: mx (the above, the default), azint (only azimuthal integration, no spot
finding/indexing), scale (re-scale/merge the already-integrated reflections in a _process.h5
without re-integrating) or calibration (detector geometry from a calibrant's powder rings, written
as a .poni file). See rugnux.
rugnux installs on its own, as the rugnux package or as a standalone archive — see
rugnux ▸ Installation.
jfjoch_extract_hkl
Extracts reflections (HKL list) from a Jungfraujoch master file; can sum the same HKL across
neighbouring images and compare against an XDS INTEGRATE.HKL reference. A developer utility: it is
built from source but, like jfjoch_recompress, is not installed into any package.
FPGA / PCIe card management
jfjoch_pcie_status
Prints detailed status information about the card. Safe to run during data collection:
./jfjoch_pcie_status /dev/jfjoch0
jfjoch_pcie_net_cfg
Reads and modifies the network configuration of the card's interfaces:
jfjoch_pcie_net_cfg <device name>
Read configuration for all network interfaces of a device
jfjoch_pcie_net_cfg <device name> <if number>|fgen
Read configuration for a particular network interface / internal frame generator
jfjoch_pcie_net_cfg <device name> <if number>|fgen ipv4 <IPv4 address>
Set IPv4 address for a particular network interface / internal frame generator
jfjoch_pcie_net_cfg <device name> <if number>|fgen direct 0|1
Set direct mode for a particular network interface / internal frame generator
jfjoch_pcie_net_cfg <device name> <if number>|fgen clear
Clear Ethernet counters for a particular network interface / internal frame generator
jfjoch_pcie_clear_net_counters
Resets the card's Ethernet, UDP and ICMP packet counters (which otherwise run from power-on):
./jfjoch_pcie_clear_net_counters /dev/jfjoch0
Testing, benchmarking and simulation
jfjoch_udp_simulator
UDP packet simulator used to test the Jungfraujoch FPGA receiver.
jfjoch_fpga_test
Exercises and benchmarks the FPGA data path and receiver. With -H it runs the high-level
synthesis C model on the CPU, so no FPGA device is required.
jfjoch_lite_perf_test
Performance test of the lite (CPU/GPU) analysis path — indexing, integration and optional file writing.
jfjoch_hdf5_test
Tests single-threaded HDF5 writer performance.
jfjoch_simplon_test
Minimal test client for a DECTRIS SIMPLON detector API.