2 Commits

Include renames

Author	SHA1	Message	Date
leonarski_f	78d3b7ef75	Stills geometry: fit only the given cell's crystal form; a stray frame is no cell population ... RefineStillsGeometry fitted distance, beam and cell on the strongest sampled frames whatever their cell, so a sample holding two crystal forms put the cell, and with it the distance, between them - while the merge later keeps only the given cell's population (GivenCellPopulation). The sampled frames are now filtered by the same population before the bundle and the module placement are formed, the population told from the strong frames (>= 20 indexed spots), whose cells show the valley between two forms; a weak frame's cell at the start geometry spreads across it. A run of one form has no valley and keeps every frame. GivenCellPopulation: a stray frame or two far out in a population's tail is a local maximum of the histogram with no valley of its own, so its range was everything, both forms included, and its mean - the mean of all frames - could sit nearer the given cell than the given form's own and win. A population is now represented only by its highest peak. Test CellPopulation_StrayFramesBeyondTheTail (fails before, passes after). Still battery, against the same code without the change: the two runs of a two-form sample -0.0019 and -0.0015 R-free (0-cycle REFMAC; the second repeated three times, -0.0013..-0.0021, run noise ~0.001), R_split 10.6 -> 9.8 % on the first; single-form controls fit the identical geometry (R-free within 0.0003). Rotation does not call either path. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit ada1b08003fa9748175cce381fc8f28569f28296)	2026-10-25 07:20:25 +01:00
leonarski_f	afbe844b20	v1.0.0-rc.178 (#88) ... * Rugnux: Processes serial crystallography data from XFELs - SACLA (MPCCD), PAL-XFEL and European XFEL (CXI), LCLS (XTC) and SwissFEL Alvra (JUNGFRAU with a CrystFEL module geometry) - with several files or Jungfraujoch master files merged in one run (`rugnux *_master.h5`). * Rugnux: Stills processing takes a known unit cell and space group as a starting point, finds the beam centre (and, with a cell, the detector distance) from the images, detects the saturation level in other facilities' files and refines the placement of individual detector panels. * Rugnux: The stills report gives R_split and CC1/2 from frame half-sets, comparable with CrystFEL. * jfjoch_viewer: Opens the same XFEL file formats. * Validation: A stills battery checks Rugnux against deposited structures from SACLA, PAL-XFEL, LCLS, European XFEL and SwissFEL. * Rugnux: More reliable convergence of rotation scaling, and live molecular replacement starts as soon as the model is uploaded. * jfjoch_broker: Initialize clears the previous dataset's bearer tokens, image buffer and live Rugnux status, and a slow CUDA JIT cache is reported at start. Reviewed-on: #88 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-10-21 11:20:01 +02:00