5 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	c93d381dc8	Error model: harden the fit against pathological inputs (code review) ... Addresses code-review findings on RefineErrorModel: - Floor the 1/dev^2 bin weight relative to the data scale (1e-3 of the median bin dev^2), not an absolute 1e-30: a near-zero-scatter bin could otherwise acquire a runaway weight and hijack the global (a,b) fit. - Reject a near-collinear normal-equation system relatively (det > 1e-10*Ass*AII) instead of with an absolute threshold that an ill-conditioned fit can pass. - Reset the model to identity at entry so any early return leaves it inactive rather than keeping a stale a/b alongside a freshly-cleared mean map (which would make CorrectedSigma fall back to the per-observation I). - PixelRefine: correct the orient_prior comment - with the sweep on, the LSQ anchor is the swept orientation (intended), not the spot-centroid one. Verified unchanged on the lyso test set (ISa 1.1, CC1/2 90.3%). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-12 18:53:02 +02:00
leonarski_fandClaude Opus 4.8	e6a50b45c7	Integration: mean background + global error model (trustworthy sigmas) ... Background estimate: use the mean of the local ring, not the median. For a right-skewed (Poisson) background the median sits below the mean, so subtracting it under-subtracts and biases every weak intensity positive; over multiplicity this becomes fake <I/sig> of a few in no-signal high-resolution shells. Fixed in both PixelRefine and BraggIntegrate2D (the classical route had the same bug). <I/sig> now tracks CC honestly and the true resolution limit is visible. Error model: fit a global a, b (XDS form sigma'^2 = a*sigma^2 + (b*I)^2) from the scatter of symmetry equivalents at the merge level (so both integrators benefit), and print it with ISa = 1/b in jfjoch_process. The (b*I)^2 term uses the reflection mean (not the per-observation I_i, which biases the weights and collapses CC); a,b come from a relative-weighted bin regression. Replaces the earlier per-resolution-shell variant, which was partly masking the background bias. METHODS.md: document both (Sections 6-7), integrator-agnostic. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-12 18:39:32 +02:00
leonarski_f	5735302691	Merge: CC1/2 limit adjustment	2026-06-09 11:06:16 +02:00
leonarski_f	32e91f7287	Minor fixes	2026-06-08 15:56:20 +02:00
leonarski_f	fc68a9baed	v1.0.0-rc.146 (#56) ... 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	2026-05-28 18:48:35 +02:00