Profiling showed the joint Ceres solve took ~120 s versus ~3.5 s for the
alternating per-image scaling loop (~35x) for no quality gain (HEWL
anomalous 0.54x vs 0.53x), so it is not worth keeping. Drop
GlobalScale.{h,cpp}, the jfjoch_process --global-scale flag, and
ScalingSettings::GlobalScaling.
While here, in the same scaling/process area: fold scale_fulls into
ScalingSettings (alongside combine_3d) so the CLI and experiment carry it
uniformly, add per-substep [timing] logging to the scaling/merge post-pass
(including the serial MergeAll vs parallel ScaleAllImages split), and carry
structured MergeStatistics + ISa in ProcessResult.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
A larger first-pass image set gives a more stable consensus lattice and so
better per-frame prediction. On HEWL crystal 2 (full 360 deg) this lifts the
anomalous S-peak height vs XDS from 0.57x to 0.61x and ISa from 10.5 to 11.0,
at negligible cost (the first pass is a small fraction of the run). ~100 is the
sweet spot; more (300) does not help further.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The rot3d combine emits fulls with partiality == 1 and image_scale_corr == 1,
so the fulls are only ever scaled as per-frame partials upstream - their
per-frame scale G is fit through the rocking-curve/partiality model
(G*partiality*B*lp*Itrue - Iobs) and so absorbs any model error. XDS/DIALS
instead scale the 3D-integrated fulls directly.
--scale-fulls inserts a second scaling pass on the combined fulls with the
Unity model (G*Itrue - I_full, no partiality term), between Combine3D and
MergeOnTheFly, reusing ScaleOnTheFly on a Unity-configured experiment copy. It
is a pure post-correction (updates the fulls' image_scale_corr 1 -> 1/G, no
re-combine).
HEWL crystal 2, anomalous S-peak height vs XDS: 0.53x -> 0.57x and ISa
9.4 -> 10.5 - improving precision and accuracy together (not the CC1/2-up /
anomalous-down trade-off of outlier rejection).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Refine all per-image scales, per-image mosaicities and the shared per-HKL
true intensities (plus the global wedge) together in one Ceres problem
(GlobalScale.{h,cpp}, GlobalScaleCeres), as an alternative to the existing
alternating merge-then-scale-each-image loop. The result feeds back into each
reflection's image_scale_corr exactly as ScaleOnTheFly does, so the rot3d
combine and MergeOnTheFly run unchanged and every metric stays comparable.
On HEWL crystal 2 the joint fit converges to the same place as the alternating
loop (anomalous S-peak vs XDS 0.53x -> 0.54x, ISa 9.4 both), confirming the
alternating path already reaches the joint optimum. Kept as a validated
alternative and the home for future global corrections.
A shared quadratic absorption surface in detector position was prototyped here
and dropped: it fit large non-physical coefficients (radially degenerate with
the per-HKL resolution structure), lowered the scaling-fit residual but raised
the error-model b (ISa 9.4 -> 7.3) and did not improve anomalous accuracy.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Reference dataset (a): LoadReferenceMtz adds column selection + cell/SG/resolution +
a data-vs-reference consistency check; jfjoch_process/jfjoch_scale gain
--reference-column; the viewer gets a Reference section in the MX settings dock
(worker-owned, independent of the loaded dataset) that flows into reprocessing jobs.
3D combine (-P rot3d): Combine3D weight-sums a reflection's per-frame partials into one
counting-limited full before merging (orthogonal ScalingSettings::combine_3d flag, not a
partiality model), with a de-biased Poisson variance. Crystal 2: ISa 1.7->8.4, R-meas
~67%->18.9%, intensities unchanged (CCref held).
Quality metrics (b): R-meas (Diederichs-Karplus) + redundancy columns in MergeStats; ISa
logged. jfjoch fulls 18.9% vs XDS 4.5% (same ASU/run).
Profile-fit integrator (experimental): ProfileIntegrate2D (--integrator gaussian|empirical)
is a reference-free, rot3d-compatible profile-fit extraction (the decomposed PixelRefine
intensity step). Gaussian: R-meas 18.9->14.6%, ISa ->9.5. Anisotropy/per-region add nothing
(the discriminating info is in the discarded rocking direction). See NEXTGEN_INTEGRATOR.md.
--dump-observations exports the unmerged fulls for XDS comparison.
Co-Authored-By: Claude Opus 4.8 <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_viewer: Add reciprocal space viewer
* jfjoch_process: Two pass algorithm that does spot finding/indexing + integration of full dataset
* jfjoch_process: Improve logic for rotation indexer, to make execution more deterministic (still work in progress)
Reviewed-on: #57
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
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.
* Support for newer CUDA architectures (notably Blackwell); minimum CUDA version 12.8
* Minor changes to jfjoch_process, jfjoch_fpga_test and jfjoch_lite_perf_test to make them more consistent
Reviewed-on: #52
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-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: Azimuthal integration mapping is generated with parallel computations, significantly reducing setup times
* frontend: Fix selection of FFTW in indexing settings
Reviewed-on: #51
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-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: For DECTRIS detectors, ZeroMQ link is persistent, to save time for establishing new connection
* jfjoch_broker: Minor bug fixes for rare conditions
Reviewed-on: #50
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: Cleanup DECTRIS start-up code to enable a shorter start time
jfjoch_broker: Allow for asynchronous start to allow overlapping detector configuration with other beamline preparations
jfjoch_broker: Goniometer axis name is converted to lowercase
jfjoch_broker: Fix bug, where wrong HTTP error codes were returned
jfjoch_broker: Improve sigma estimation during merging (K. Takaba)
---------
Co-authored-by: takaba_k <kiyofumi.takaba@psi.ch>
Reviewed-on: #48
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-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: Better track time for each operation in the processing stack
* jfjoch_broker: Rewrite preprocessing of diffraction images in the non-FPGA workflow to better use GPUs (work in progress)
* jfjoch_broker: Remove ROI calculation in the non-FPGA workflow (work in progress)
* jfjoch_viewer: Toolbar displays image number starting from 1 (instead of 0)
Reviewed-on: #46
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: Improve logic regarding indexing architecture and thread pools (work in progress).
Reviewed-on: #45
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
Updates to CI pipeline
* New docker image for Ubuntu 22.04 with CMake 3.26
* New docker image for Rocky 9 with DIALS 3.27
* New automated test to check for DIALS processing with xia2.ssx
Reviewed-on: #42
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: Use httplib for HTTP server instead of Pistache
* jfjoch_broker: Drop OpenSSL support
* jfjoch_broker: Base work for multi-lattice support in the future
* Update dependencies to more recent versions (spdlog, HDF5, Catch2, httplib)
Reviewed-on: #41
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.124.
* jfjoch_broker: Fix bug in saving JUNGFRAU calibration (pedestal/pedestalRMS)
* jfjoch_viewer: Fix calibration (pedestal) images being open flipped
* jfjoch_process: Add space group detection (EXPERIMENTAL)
Reviewed-on: #39
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.124.
* jfjoch_broker: Rotation indexer has two retries if failes
* jfjoch_broker: Rotation indexer handles small number of rotation images (like test shot)
* jfjoch_broker: Integration calculates background mask based on R2 radius
* jfjoch_process: HDF5 files are not saved by default
Reviewed-on: #37
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.124.
* jfjoch_broker: Handle properly reuse of image buffer locations
* jfjoch_broker: Fix bug in counting idle slots
* jfjoch_broker: Force obtuse angle for monoclinic cells
* jfjoch_process: Change scaling refinement tolerance
Reviewed-on: #35
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-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.124.
* jfjoch_broker: Default EIGER readout time is 20 microseconds
* jfjoch_broker: Multiple improvements regarding performance
* jfjoch_broker: Image buffer allows to track frames in preparation and sending
* jfjoch_broker: Dedicated thread for ZeroMQ transmission to better utilize the image buffer
* jfjoch_broker: Experimental implementation of transmission with raw TCP/IP sockets
* jfjoch_writer: Fixes regarding properly closing files in long data collections
* jfjoch_process: Scale & merge has been significantly improved, but it is not yet integrated into mainstream code
Reviewed-on: #34
This is an UNSTABLE release. If things go wrong with analysis, it is better to revert to 1.0.0-rc.124.
* jfjoch_broker: Fix bug for monoclinic space groups being wrongly refined when beta is much different from 90 deg.
Reviewed-on: #33
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
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. This version significantly rewrites code to predict reflection position and integrate them,
especially in case of rotation crystallography. If things go wrong with analysis, it is better to revert to 1.0.0-rc.123.
* jfjoch_broker: Improve refection position prediction and Bragg integration code.
* jfjoch_broker: Align with XDS way of calculating Lorentz correction and general notation.
* jfjoch_writer: Fix saving mosaicity properly in HDF5 file.
* jfjoch_viewer: Introduce high-dynamic range mode for images
* jfjoch_viewer: Ctrl+mouse wheel has exponential change in foreground (+/-15%)
* jfjoch_viewer: Zoom-in numbers have better readability
Reviewed-on: #31
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 and not recommended for production use (please use rc.11 instead).
* jfjoch_broker: Experimental rotation (3D) indexing
* jfjoch_broker: Minor fix to error in optimizer potentially returning NaN values
Reviewed-on: #18
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.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 4.8
