leonarski_fandClaude Opus 4.8
cbc6a85157
The serial-stills merge (MergeOnTheFly::CorrectedSigma) weighted each observation by 1/sigma^2 using the observation's OWN sigma. Below ~1 photon the Poisson signal part of that sigma correlates with the observation's up/down fluctuation, so the inverse-variance mean is biased low: an up-fluctuated observation acquires a larger sigma and is over-downweighted. The rotation combine (RotationScaleMerge:: process_rawrun) already avoids this by rebuilding the signal variance at the pooled estimate; the stills path did not. Decompose each observation's variance into a background/read part (kept per-observation) and a Poisson signal part, and rebuild the signal part at the reflection's expected <I>. Bit-identical when an observation sits at its reflection mean; only weak-shell weights move. Now default on, so the stills path matches the rotation path; --no-expected-variance-merge restores the old observed-sigma weighting. Validated by paired refinement (phenix, 5 free-set seeds, byte-identical free flags across arms): R-free-neutral on strong lysozyme and lower R-free on weak serial-stills data checked against an independent deposited model (6/6 seeds). The CC1/2 dip on strong data reflects precision, not accuracy. Applies to both offline rugnux and the online broker stills merge. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Jungfraujoch
Application to receive data from the PSI JUNGFRAU and EIGER detectors.
All documentation is now placed in docs/ subdirectory and for the current version hosted on Jungfraujoch Read The Docs page.