dataset_settings gains beam_size_x_um and beam_size_y_um, the horizontal and
vertical size of the X-ray beam where it meets the sample. They follow the same
route total_flux takes - OpenAPI, DatasetSettings, the CBOR start message, the
HDF5 master, and back out of a stored file - and nothing consumes them; this is
metadata a beamline can state and a downstream program can read.
NXmx puts this in the application definition rather than the base class: not
NXbeam's extent (rank 2, nP x 2, per scan point, always FWHM of a rectangular
aperture) but NXmx's own incident_beam_size, a recommended rank-1 two-element
array in the order x, y. Both are live and neither is deprecated, so the choice
matters; the MX definition wins in an MX file. Written as one array with a
units attribute of "m", like every other length in the master, so the settings
hold micrometres and FillMessage converts once.
The unit table of ReadLength_m becomes LengthUnitFactor so the array read can
share it: a master written elsewhere may state this in millimetres.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
The adopted space group travelled the pipeline as a bare int and was rebuilt
downstream with find_spacegroup_by_number, which returns the reference setting.
So every setting a number cannot name was destroyed one line after it was
determined: P 1 1 2 came back as P 1 2 1, I 1 1 2 as C 1 2 1, R 3:R as R 3:H.
DatasetSettings now holds the gemmi::SpaceGroup itself, DiffractionExperiment
exposes it as GetGemmiSpaceGroup() / GetSpaceGroupOrP1(), and everything that
used to take an int - HKLKeyGenerator (its int constructor is gone, so the
compiler finds the callers), the merge, the R-free flags, French-Wilson, the
reindexing ambiguity, the completeness enumeration, the MTZ and mmCIF exports,
the model validation - takes the group. -S keeps the setting the symbol names
rather than reducing it to a number.
The end message carries both spellings and a reader prefers the name, since
only the name keeps the setting while the number is what a reader written
before the name understands. It carries them over CBOR too: the determined
group was never serialised at all, so a group rugnux chose reached the master
file only when the same process wrote it, and an online writer fell back to
whatever the user had supplied at the start. Both keys are optional additions,
so an older reader skips them and a newer one reads an older sender.
On disk the master's /entry/sample/space_group carries the extended
Hermann-Mauguin name and is what the reader takes the group from, so a setting
survives a _process.h5 and the --mode scale that re-reads it; the number stays
beside it and is the fallback for files written before. Every one of the 230
reference settings the old writer could produce reads back as itself, so older
files are unaffected.
Stage A and Stage B of the search still enumerate reference settings only, so
this determines no group differently today - it is what the enumeration needs
before it can be widened.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
**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>
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.
* Analysis: The azimuthal-integration solid-angle correction now follows the incidence angle to the detector normal (`cos^3` of that angle) instead of `cos^3(2*theta)`, so it is correct for a tilted detector and matches PyFAI `solidAngleArray` and MAX IV azint (unchanged for an untilted detector). Crystal geometry refinement (`XtalOptimizer`) no longer silently ignores an imported PONI `rot3` (rotation about the beam): it is applied as a fixed rotation in the residual so refinement stays consistent with the rest of the pipeline. Polarization and azimuthal binning already honoured `rot3` through the full PONI rotation.
* jfjoch_viewer: Open datasets on the WSL2/UNC filesystem (paths starting `\\`); write processing outputs next to the input file, with a Browse button and independent `_process.h5` / merged `.mtz`/`.cif` toggles; and show the determined space group in the merge-statistics window.
* rugnux: Accept an absolute `-o` output prefix in offline processing.
* Packaging: The self-contained Linux viewer `.tgz` now bundles cuFFT, so it runs without a system CUDA toolkit (`.deb`/`.rpm` are unchanged, distro-managed).
* Docs: Bring the analysis references up to date with the code. `docs/CPU_DATA_ANALYSIS.md` now reflects the unified profile-fit Bragg integration engine, multi-lattice indexing, azimuthal phi binning, the radial parallax/bandwidth profile with sub-pixel centring, the rot3d capture-fraction handling and the automatic CC1/2 resolution cutoff, and drops the descriptions of features that were never implemented (French-Wilson amplitudes, the still excitation-error partiality model); `docs/RUGNUX.md` documents the new `--resolution-cutoff`/`--resolution-cc-target`/`--resolution-shells`, `--min-captured-fraction`, `--mosaicity`, `--reference-column`, the azimuthal correction toggles and the geometry-override options, and corrects the `-N` default. The outdated in-source design notes (ICE_RING_DETECTION, BRAGG_INTEGRATION_ENGINE, NEXTGEN_INTEGRATOR) are removed.Reviewed-on: #68
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
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.
* jfjoch_process: Major rotation (rot3d) data processing overhaul - robust profile-fit integration, Cauchy-loss scaling with optional absorption surface, de-novo indexing and space-group/centering determination fixes, and merging statistics + ISa in the mmCIF output.
* jfjoch_process: Add EXPERIMENTAL ice-ring detection (--detect-ice-rings) that excludes ice reflections from scaling.
* Compression: Add BSHUF_ZSTD_RLE_HUFF, make compression size-aware (drop frames that don't fit rather than aborting), and add the jfjoch_recompress tool.
* jfjoch_viewer: Report "Multiple lattices detected" and grey out "Analyze dataset" on a live connection.
* jfjoch_broker: Write smargon chi/phi goniometer positions to NXmx; read sensor thickness/material from HDF5 metadata.
* CI: Build Windows (CUDA and non-CUDA) installers.Reviewed-on: #66
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
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.
* jfjoch_broker: Add EXPERIMENTAL pixelrefine mode for image processing
* jfjoch_broker: Allow to load user mask from 8-bit and 16-bit TIFF files
* jfjoch_broker: Add ROI calculation in non-FPGA workflow
* jfjoch_broker: Fixes to TCP image pusher
* jfjoch_broker: Remove NUMA bindings
* jfjoch_broker: Improvements to indexing
* jfjoch_broker: For PSI EIGER, trimming energies are taken from the detector configuration (now compulsory) instead of hardcoded values
* jfjoch_writer: Save ROI definitions and the per-pixel ROI bitmap in the master file; azimuthal ROIs support phi (angular) sectors
* jfjoch_viewer: Major redesign with dockable panels and saved layouts, plus on-canvas creation/move/resize of box, circle and azimuthal ROIs
* jfjoch_viewer: Run jfjoch_process reprocessing jobs from inside the GUI and overlay per-run results
Reviewed-on: #63
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. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132.
* Multiple small bug fixes scattered across the whole code base. (detected with GPT-5.4)
* jfjoch_viewer: Improve image render performance
Reviewed-on: #44
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
leonarski_fandClaude Opus 5