4 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	d891551127	rugnux: make model validation batch-consistent for fragment screening ... Reworks the --model / French-Wilson / R-free path so a batch of datasets of one crystal form yields comparable maps and a shared test set, and fixes a French-Wilson prior bug. - French-Wilson: fix inverted centric/acentric prior - the call passed !centric into the selector, swapping the two Wilson forms for every weak reflection. Add a test pinning a centric weak |F| below an acentric one. - R-free flags: assign by a pure per-hkl hash instead of a per-dataset resolution-shell stratification, so every dataset of one crystal form gets the same free set (needed for ensemble refinement / PanDDA). Still a pure function of the Laue-ASU key, so Bijvoet/symmetry mates never split. - R-free flags: import a reference MTZ's FreeR_flag column when present (CCP4 test=0, auto-complement for a phenix-style test=1), so a whole campaign inherits one shared test set. New ApplyReferenceFreeFlags, wired post-merge in both the full-analysis and --scale paths. - Model maps: scale the model with an overall scale, anisotropic B and flat bulk solvent only - drop the free-form per-shell K(1/d^2) rescale, which reshaped each dataset's radial amplitude profile differently and made a batch of maps non-comparable. - Merohedral indexing: model validation resolves the ambiguity by lowest R-free only when there is no reference; with a reference MTZ the indexing is already resolved against it (merge stage / stills scaling) and that authoritative choice is kept. - Remove a stale <algorithm> include; update docs and changelog. Tests: french_wilson, rfree, reference_mtz (new), reindex, hkl_key all pass. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-13 11:31:33 +02:00
leonarski_fandClaude Opus 4.8	87af0f419b	scale_merge: compute French-Wilson amplitudes at end of merge, write them alongside intensities ... Merged reflections carried only intensities; a naive sqrt(max(I,0)) turns every weak or negative measurement into a biased (or zero) amplitude. Add a French-Wilson step so the merged reflections themselves carry proper Bayesian amplitudes. New FrenchWilson.{h,cpp}: ApplyFrenchWilson() fills F and sigmaF on each MergedReflection with the posterior mean |F| given I and its sigma under the Wilson prior: - correct centric vs acentric prior (gemmi is_reflection_centric); - epsilon (symmetry-enhancement) multiplicity: the shell mean is <I/eps> and the prior mean for a reflection is eps * <I/eps>; - numerically stable log-shift integration of the posterior; - strong reflections (I > 4 sigma) short-circuit to sqrt(I) where the FW bias is negligible; - unusable I/sigma falls back to sqrt(max(I,0)). It runs as the last step of the merge routine (both MergeOnTheFly and RotationScaleMerge), so F/sigmaF are part of the merged result and downstream consumers (file writing AND, later, map calculation) all use the same amplitudes rather than each recomputing FW and risking divergence. The writers just emit the fields; extended additively: - MTZ: F (F) + SIGF (Q) columns; - mmCIF: _refln.F_meas_au / _refln.F_meas_sigma_au; - HKL text: F sigmaF appended (rfree flag kept in place for back-compat). Existing intensity columns are unchanged, so current readers keep working while phenix.refine (etc.) can now refine against the amplitudes. Verified on lyso (1.3 A): all 173 negative-intensity reflections get F>0, strong reflections have F/sqrt(I)=1.000, no NaN, and the mmCIF _refln loop is well-formed. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-12 21:27:44 +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
leonarski_f	1ab257af6c	v1.0.0-rc.125 (#32) ... 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>	2026-02-18 16:17:21 +01:00