4 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Fable 5	347228d008	jfjoch_process: azimuthal-integration CLI + default 0.01 1/A q-spacing ... Add -q/--azim-q-spacing, --azim-min-q, --azim-max-q, --azim-phi-bins (mirroring jfjoch_azint) so offline processing can set the radial binning, applied before the azint mapping is built. Set the AzimuthalIntegrationSettings default spacing to 0.01 1/A (was 0.05): the coarse default barely resolved the narrow ice rings, diluting the ice-ring score. Finer binning sharpens it a lot with no effect on processing - EP_cs_01-17 ice score 4.6->7.3 (max 11->23), clean cytC stays ~1.0, and space group / cell / ISa / completeness are unchanged (cytC, InsI3, MyoB, pding4_001 verified full-image). Documented in JFJOCH_PROCESS.md. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>	2026-07-02 17:24:05 +02:00
leonarski_fandClaude Opus 4.8	ed9f6ac9eb	integration: remove --reciprocal-profile (proven per-frame dead-end) ... An 11-crystal mosaicity-stratified re-test (/data/rotation_test, off vs on vs a de-contaminated variant, plus a per-frame dump of the fitted widths) showed the dial is net-negative and cannot work in the per-frame paradigm: - The C|q|^2 mosaicity term - the whole point - is unfittable per-frame: the fitted curvature a2 comes out ~0 (often negative) on every crystal, with zero correlation to the XDS mosaicity (0.09..0.42 deg). Strong spots sit at low q where eta^2 q^2 is invisible; the curvature only appears at high q where there are ~0 strong spots. The law degenerates to a straight line. - With a2~0 the high-res width becomes a blind 1/cos^2(2theta) extrapolation, 2-4x wider than per-shell. The per-shell path's high-res "starvation" (flat narrow fallback) is accidentally correct: weak, crowded high-res spots want a narrow aperture, not the true wide spot shape. - The over-wide profile pulls background into weak spots -> R-meas rises, CC1/2 drops in reliable high-multiplicity shells (pding4_001, pding4_003, MyoB, EcwtCQ066). A cap at the widest well-sampled per-shell width recovers the regression, confirming over-widening is the harm. No crystal reliably wins; the apparent overall-CC gains were all in noise shells (mult 2-3, CC<20%). Delete the CLI flag, the BraggIntegrationSettings::reciprocal_profile setting, and the per-frame fit block. Default (per-shell) integration is byte-identical. NEXTGEN_INTEGRATOR.md records the finding as a dead-end for posterity. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-02 11:39:09 +02:00
leonarski_fandClaude Fable 5	7e3ad84a5b	jfjoch_process/scale: default to mmCIF, auto-detect rotation, rot3d partiality ... - Default reflection format is now mmCIF (ScalingSettings.h, the single source of truth). jfjoch_process and jfjoch_scale no longer hard-code a local MTZ default; they override only when --scaling-output is given. jfjoch_viewer inherits this. - A dataset with a rotation goniometer axis is processed as rotation data (two-pass indexing) by default; add --process-as-stills to force per-frame stills. -R still tunes the first-pass image count. - rot3d is the default partiality model for rotation processing (fixed for stills) when no explicit -P is given. - Update docs/JFJOCH_PROCESS.md: new de-novo rotation/stills examples, corrected -R/-P/--scaling-output defaults, --process-as-stills, and a real Integration table. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>	2026-07-02 08:34:50 +02:00
leonarski_f	75e401f0e5	v1.0.0-rc.153 (#63) ... 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	2026-06-23 20:29:49 +02:00