The per-image ice_ring_score was written to the data files (HDF5DataFilePluginMX)
but the master-file write and the stored-file read path were missing, so opening a
processed HDF5 (e.g. in jfjoch_viewer) would not surface it. Mirror bkg_estimate:
write /entry/MX/iceRingScore in the NXmx master (HDF5NXmx, from EndMessage), and
read it back in HDF5MetadataSource into the dataset (master + data-file reads) and
per image into the message. Verified the write; the read is a byte-for-byte mirror
of the working bkgEstimate round-trip.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Add an optional Smargon static positioner (chi/phi angles + rotation axes)
that is reconstructed into the NXmx sample transformation chain. Chi/phi are
appended at the innermost end of the chain (closest to the sample) for both
the goniometer and grid-scan branches, with axes defaulting to chi {0,0,1}
and phi = omega default {1,0,0}.
- SmargonPosition gains chi_axis/phi_axis (common/JFJochMessages.h)
- OpenAPI: optional phi_axis/chi_axis arrays; clients regenerated
- OpenAPIConvert wires Dataset_settings.smargon -> DatasetSettings
- CBOR serializer/deserializer round-trip the axes
- tests: CBORSerialize_Start_Smargon
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Space-group search (image_analysis/scale_merge/SearchSpaceGroup):
- Two-stage POINTLESS-style determination. Stage A scores each distinct rotation
operator once (was once per candidate space group, ~34x faster on lysozyme:
~26s -> <1s) and picks the largest point group all of whose operators confirm.
Stage B picks the maximal space group whose predicted absences are confirmed
weak, fixing the prototype's default to the symmorphic group (it returned P422
instead of P4(3)2(1)2). Enantiomorphic / origin-ambiguous pairs (P4(1) vs P4(3),
I222 vs I2(1)2(1)2(1)) are reported as indistinguishable.
- Constrain candidates to subgroups of the lattice (metric) holohedry and weigh
centering only P-vs-metric, fed from rotation indexing's LatticeSearch result.
Integration / pipeline:
- With no user-fixed space group, predict in P (IndexAndRefine) so the
centering-absent reflections are integrated and the search can confirm/deny
centering (catching pseudo-centering / a missed superstructure) instead of
trusting the metric; a user-fixed group still rejects absences in integration.
- JFJochProcess: scale+merge in P1 -> determine the space group -> set it and
re-scale+merge in it (statistics then come out in the right symmetry) -> write
it to /entry/sample/space_group_number (new EndMessage.space_group_number,
preferred by NXmx::Sample). jfjoch_scale no longer searches; it consumes the
file's space group (and no longer clobbers it with an empty -S).
Twinning (new image_analysis/scale_merge/TwinningAnalysis): Padilla-Yeates L-test
(<|L|>, <L^2>; acentric-only, positive intensities so L is bounded) plus a
shell-normalised <I^2>/<I>^2 second moment and a twin-fraction estimate. Reported
after the final merge in jfjoch_process and jfjoch_scale, and surfaced in the
jfjoch_viewer merge-statistics window with a red outline when twinning is suspected.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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 for data processing - in case of troubles go back to 1.0.0-rc.144.
* jfjoch_broker: Improve azimuthal integration (add <I^2> calculation)
* jfjoch_broker: Fixes around indexing, aiming to handle multi-lattice crystals (work in progress, it is not fully integrated)
* jfjoch_writer: Save mean(I), stddev(I), and count(I) for each azimuthal bin
Reviewed-on: #58
This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144.
jfjoch_process: Generate a dedicated file (_process.h5), which can be used as a replacement for the _master.h5 file for a reanalyzed dataset.
jfjoch_process: Improve the performance of scaling and merging, implement on the fly scaling.
jfjoch_writer: All final data analysis results are repopulated in the _master.h5 file.
jfjoch_scale: Dedicated tool for rescaling/merging existing data.
jfjoch_viewer: Fix bugs where pixel labels where displayed on a wrong pixel.
WARNING! Scaling and merging are experimental at the moment, and may not provide reasonable results for the time being.
Reviewed-on: #56
This is an UNSTABLE release. The release has significant modifications for HDF5 writing logic - in case of troubles go back to 1.0.0-rc.144.
* **Default HDF5 writing mode is with VDS, not soft-links** - this improves DIALS compatibility and makes format more future-proof, NXmx legacy format might be phased-out in the future.
* XDS plugin: Improve performance of VDS reading.
* jfjoch_writer: Significant improvement on how file systems I/O are handled through a dedicated pass-through VFD.
* jfjoch_writer: Clean-up of HDF5 routines to better handle issues.
Reviewed-on: #55
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: Add better locking for detector object - should help, when detector initialization takes too long
* jfjoch_writer: Enable writing single, integrated HDF5 file with both data and metadata
* XDS plugin: Add generation of Jungfraujoch plugin for XDS
* CI: Add tests with XDS and DIALS (`xia2.ssx`)
Reviewed-on: #43
This is an UNSTABLE release. This version adds scalign and merging. These are experimental at the moment, and should not be used for production analysis.
If things go wrong with analysis, it is better to revert to 1.0.0-rc.124.
* jfjoch_broker: Improve logic on switching on/off spot finding
* jfjoch_broker: Increase maximum spot count for FFBIDX to 65536
* jfjoch_broker: Increase default maximum unit cell for FFT to 500 A (could have performance impact, TBD)
* jfjoch_process: Add scalign and merging functionality - program is experimental at the moment and should not be used for production analysis
* jfjoch_viewer: Display partiality and reciprocal Lorentz-polarization correction for each reflection
* jfjoch_writer: Save more information about each reflection
Reviewed-on: #32
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
This is an UNSTABLE release and not recommended for production use (please use rc.111 instead).
* jfjoch_broker: Improve handling of rotation indexing
* jfjoch_broker: More information saved in CBOR end message (WIP)
* jfjoch_writer: Save rotation indexing lattice parameters and Niggli class
* jfjoch_viewer: Remove (for now) primitive cell information
Reviewed-on: #19
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
This is an UNSTABLE release.
jfjoch_writer: Fix and improve the way grid scan geometry is saved (non-NXmx extension makes it way easier)
jfjoch_viewer: Display grid scan results in 2D (work in progress)
jfjoch_viewer: Improve auto-scaling on start of images (work in progress)
jfjoch_viewer: Add B-factor and resolution estimate to the dataset info plots
Reviewed-on: #9
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
This is an UNSTABLE release.
* Fixes in CI pipeline
* jfjoch_broker: Remove PNG preview, no dependency on libpng
* jfjoch_writer: Fix UTC timestamp being generated wrong (mix between milli- and microseconds)
* jfjoch_viewer: Show data collection time in dataset tooltip
* jfjoch_viewer: Allow to choose the calibrant (presets for LaB6 and silver behenate)
* jfjoch_viewer: Auto foreground value
* Use external libjpeg-turbo and libtiff: simpler build stack, these are built and linked statically in automated Docker builds
* Remove OpenBLAS dependency
Reviewed-on: #1
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
leonarski_fandClaude Fable 5