2 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	a29c36600f	Beam-stop shadow detection, and a low-resolution limit for scaling ... rugnux finds the beam stop and its holder in a projection of 60 images and marks them in the pixel mask as bit 9 (--detect-beam-stop[=N|off], on by default). Reflections behind the stop are attenuated but not flagged, so they integrate low with a plausible sigma and nothing downstream catches them: the signal-box gate requires 100% valid pixels and shadow pixels are valid, the background clip is high-side only, and the |zeta| cut applies only to the space-group search merge. The detection compares each pixel's background against the typical background at the same radius on two channels. An azimuthal one (the ring median) finds the holder arm, which is a minority of its ring; a radial one (the background just outside) finds the disk, which the ring median cannot see because inside a fully blocked ring the median is the shadow itself. Pixels are pooled over a 5x5 box and tested only where the background has actually been counted, so low-background data no longer masks the whole detector. Recorded reflections are carved back out - a beam stop cannot block a reflection that was measured. Bit 9 belongs to the run that found it, not to the dataset: it is cleared when a run starts, so a mask read back from a file that carries one starts clear. The user mask (bit 8) is left alone. Scaling and merging gain a low-resolution limit, default 50 A (--scaling-low-resolution <num>, 0 removes it), applied per observation before scaling so it also protects the per-frame scale fit and the space-group search. 50 A is the value XDS configurations use; rugnux_vs_xds.py now matches both of XDS's resolution limits instead of only the high one, so the lowest shell is the same shell in the two programs. The viewer draws the detected shadow in coral with a "Show beam stop" switch in the side panel, exposes the low-resolution limit in the settings dock, and offers detection in its processing jobs. Adding an image marker meant giving the reader a MIN_REAL_PXL_VALUE, because several places classify a pixel by range rather than by equality and would otherwise read the new marker as a very negative intensity. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-09 01:05:31 +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