A writer refusing to overwrite an existing file was reported badly, and the
earlier fix only covered half of it. The commit message of a6a715703 states the
assumption that broke: "SendStartMessage precedes every std::async in the
receiver constructor". That is true of JFJochReceiverFPGA, where the start
message goes out from the constructor body, and false of JFJochReceiverLite,
where it goes out from MeasurementThread - launched by std::async from the
constructor, which waits only on data_analysis_started. On the DECTRIS path the
writer's refusal therefore cannot reach services.Start(); it arrives from
services.Stop(), i.e. the second try-block of the state machine's
MeasurementThread, which never touched start_exception. /wait_till_done answered
200 for a run that never wrote anything.
Two changes, in front of the problem and behind it.
In front: a PREFLIGHT frame (TCP protocol version 3 -> 4), sent to every writer
before the receiver is built and before the detector is armed. It carries the
same CBOR start message a START does and asks one question: could this run be
written? The writer runs FileWriter::Preflight - the first three statements of
the FileWriter constructor, stopping short of the only one that creates
anything - and answers with an ACK. Shared code, so a pre-flight that passes
cannot be contradicted by the start behind it. A refusal is not fatal: nothing
was started, the connection stays usable, and above all no series is left armed
waiting for a trigger that will not come. Both ends already reject a frame of
another protocol version, so the bump costs no compatibility.
The check now covers the data files, not only the master. A stale
_data_000001.h5 used to sail through and fail when the file was renamed into
place at the end of the run, after the whole dataset had been collected. The
writer holding the master file checks for all of them - they share a directory
by construction, the master linking them by relative name - so the siblings do
not race each other statting files the others are creating.
Behind: /wait_till_done maps an Idle state to 200 or 500 by the severity of the
end-of-run message, so a collection that lost packets, or whose writer could not
write, is no longer indistinguishable from a good one to a script. A cancelled
collection is not affected - MeasurementThread checks the cancel before it looks
at the completeness of the data, and reports it with Info severity - and a
warning is still a 200. start_exception is untouched.
The PREFLIGHT payload is built from FillMessage alone, which is what keeps it
small: the per-pixel arrays are added by SendStartMessage and are not in it.
Measured on a JUNGFRAU 9M, 1.4 kB against 543 kB for the start message. It is
deliberately the whole of FillMessage rather than the fields the check reads
today - a hand-picked subset would answer for a different set of file names the
day the check learns to read one more field, and would do it silently.
Three defects found on the way:
TCPImagePuller republished a PREFLIGHT as a real start message, announcing to
downstream consumers a run that was not going to happen.
TCPStreamPusher::run_number was a plain uint64_t written by the control thread
and read by every ACK thread; Preflight adds a second writer to it.
StreamWriter::CollectImages reprocessed the last frame whenever WaitForImage
returned false - run is only tested at the top of the loop - so an abort wrote
the last image a second time. Pre-existing; the new branch made it visible.
Verified against a running broker on the local configuration: a colliding master
file and a colliding data file are both refused by /start, /wait_until_running
and /wait_till_done with the writer's own message, and the log shows the receiver
was never started for either; a cancelled collection still answers 200.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_016WmryXe8ASbNi632sUMfsa
* 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>
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.132.
* jfjoch_broker: Further reduce startup time for DECTRIS detectors by selectively modifying SIMPLON parameters on `/start`
* jfjoch_broker: Further reduce startup time for DECTRIS detectors by not setting beam center and detector distance via SIMPLON API on '/start'
* jfjoch_broker: Add an extra message to ZeroMQ puller ready to monitor Lite worklow preparation time
* jfjoch_broker: Image buffer configuration is postponed for Lite receiver flow till start message is received
* jfjoch_broker: Use nanoseconds internally for frame/image/readout time
* jfjoch_broker: Extra messages added for receiver operation (to be removed after debugging finished)
* jfojch_broker: Improve profiling of different data analysis steps
* jfjoch_broker: Record integration reflection count
* jfjoch_broker: Fix bug where ZeroMQ preview frequency was confusing time units (micro vs. milliseconds)
* jfjoch_broker: Fix bug where '/wait_till_done' got deadlocked
* jfjoch_writer: Fix confusion between NaN and zero in floating-point datasets
**Breaking changes**: detector definition is now using nanoseconds to define minimum frame time, minimum count time and readout time.
Reviewed-on: #49
This is an UNSTABLE release and not recommended for production use (please use rc.96 instead).
* jfjoch_broker: For DECTRIS detectors add dark data collection during initialization for bad pixel mask
* jfjoch_broker: Refactor of calibration logic for more clear code (likely to introduce problems)
* jfjoch_viewer: Add option to handle user pixel mask (experimental)
* jfjoch_viewer: More options for ROI
* jfjoch_viewer: Add window to display calibration
Reviewed-on: #2
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
leonarski_fandClaude Opus 5