The per-image ice score was read off the PLAIN azimuthal profile. That profile is a
per-ring mean, so a few strong Bragg reflections landing in a ring's q bin lift it
exactly as ice would. Measured over 37 rotation crystals, that did not merely add
noise - it INVERTED the metric: the two highest-scoring crystals had no ice at all
(4.23 and 4.06), while a clean control read 1.57. A decoy null - the identical
statistic evaluated at q positions where hexagonal ice cannot be - reaches 1.51 at its
99th percentile and 2.70 at its maximum, so that metric cannot support any absolute
threshold whatsoever.
The adaptive spot finder already computes the right input for its own threshold: a
sigma-clipped per-resolution-ring background, in the same bins. A powder ring is
azimuthally smooth and survives the clip; Bragg peaks do not. On the clipped profile
the clean population tightens to 1.00-1.22 and the crystals with confirmed ice sit at
2.08-2.37, against a decoy null that never exceeds 1.29.
That channel is blind to one thing: ice in large crystallites diffracts as DISCRETE
spots and leaves the radial profile flat. So a second channel counts found spots on the
rings against the same q width of ice-free flanks beside them. The two barely overlap -
the smooth-ice crystals read 2.1-2.4 / ~1.0 and the textured ones ~1.1 / 3.8-17.6,
while a clean crystal reads 1.04 on both.
Both are then used as a GATE (--ice-min-score 1.5, --ice-min-spot-ratio 2.0, both
calibrated on the battery, 0 disables): the eleven fixed hexagonal bands cover 16-26 %
of the unique reflections at typical resolutions whether or not the crystal has ice, so
flagging, the exclusion from the scale fit and the merge-time CC1/2 ring mask are now
all skipped when neither channel sees any. The gate is applied in the full pipeline and
in --scale, which reads the stored per-image values back out of the _process.h5.
Also fixes the merge-time mask's control: the shoulder now excludes reflections that
are themselves on an ice ring. The rings are not evenly spaced - 1.947/1.916/1.882 A
sit 0.05-0.06 apart in q - so for those three the [w,3w) shoulder landed squarely on
the neighbours and the test compared ice against ice. Measured, that is the only thing
this changes: it removes firings on those three rings and leaves every other firing's
CC pair identical to three decimals.
And the online ice half-width, which was 0.02 in the API against 0.03 offline, so the
same data got a narrower band online than the measured ~0.06 ring FWHM justifies.
Battery (37 rotation crystals, against the previous behaviour): space groups 34/37 in
both and NO crystal's space group changes; 6 crystals gain unique reflections, 1 loses.
Best of them gains 7082 unique reflections with R_meas 16.0 -> 14.3, CC1/2 95.9 -> 97.3
and ISa 13.7 -> 19.0; another goes R_meas 54.9 -> 42.9, CC1/2 84.0 -> 90.4, ISa
3.9 -> 5.5; a third reaches CC1/2 99.4 from 95.7 at an unchanged reflection count. The
one crystal that loses reflections improves on both R_meas and CC1/2.
Not done here: the ScanResult/API/plot-type/frontend/viewer layers for the new
spot_count_ice_control (they need the OpenAPI regeneration). Message, CBOR, HDF5
write/read and the receiver plots are.
Co-Authored-By: Claude Opus 5 (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_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. 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 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>
leonarski_fandClaude Opus 5