5 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	70e11d9ab8	rugnux pre-scan: projection and defective pixels per card, the sample read once, beam stop memoised ... The beam-stop projection (ShadowAccumulatorGPU) and the defective-pixel sums (HotPixelFinderGPU) are now kept one per card, fed by workers pinned t % gpus like the other pre-scan workers, and folded into the first card when they are read (cudaMemcpyPeer + an integer add / max-with-count kernel). All of them are integer sums or a maximum with the first-value rule, so the fold is order-free and the result is identical to one card's. With one card nothing is folded. The pre-scan sample is read once and kept (compressed as stored; up to 2 GiB, a frame past that is read again where it is wanted) for the spot measurement and the defective pixels, which read every frame again each before - a CBF/marCCD/SMV frame was decoded on the host three times. A beam-stop detection that finds no shadow leaves the mask as it was, so every probe copy of the run repeated it on the same inputs. Its answer (shadow, ring centre, mean projection) is now kept in a memo shared with the copies, keyed on the sampled frames, the geometry the rings are drawn in, the polarization and the binary mask; up to 4 entries. Debug TIMING lines for the pre-scan's parts (read and projection, beam stop, defective pixels, spot measurement). New tests: two accumulators/finders folded match one fed every frame. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EizBKhTqrAYago9KJG3dA3	2026-10-12 08:11:05 +02:00
leonarski_fandClaude Opus 5.5	1bb6d59bf7	HotPixelFinder: mask dead pixels, and run on CCD sweeps too ... A pixel that reads at most half of its own sector's level on average, by more than the bound a hot pixel's excess has to clear, is now masked as dead - the mirror of the hot rule. Nothing but a defect keeps a pixel dark frame after frame, and every reflection whose disk covers it is integrated short. The finder now also runs on CCD sweeps (no sensor depth): a dead CCD pixel reads its offset, far below any ring with background, and the hot rule's ten-fold ratio does not depend on Poisson counts either. Found on 5jk4 (ADSC Q4, 2304x2304): the last row and the first two columns read the offset (~20 ADU against ~60-100 around them) and were unmasked. Reflections touching them merged to large negative intensities, and one observation at y=2298 with sigma 10334 swamped the outer shell's half-set CC1/2 (3.9 %) and the overall CC1/2 (0.786; 0.998 at rc.174). With the 6630 dead pixels masked the fall-off is clean: CC1/2 0.998, cut 0.96 A (fit 1.01 A), at --prepass-fraction 0.5 and 1 alike. Counting-detector sets with low background are untouched (myoglobin X06DA: 0 dead). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi	2026-10-08 06:53:40 +02:00
leonarski_fandClaude Opus 5.5	08ca1d5764	Move the hot-pixel finder from rugnux/ to image_analysis/hot_pixels/ ... A pure move: HotPixels.{h,cpp} and HotPixelsGPU.{h,cu} are compiled into JFJochImageAnalysis (like beam_stop/) instead of JFJochRugnux. Only include paths and the CMake source lists change; the objects are unchanged. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi	2026-10-07 14:05:37 +02:00
leonarski_f	a395f358ef	1.0.0-rc.174 (#84) ... * Rugnux: Performance improvements on GPU and CPU (more of the pre-scan and of scaling on the GPU, faster CPU spot finding and crystal refinement), with unchanged results. * Rugnux: More robust processing - patches of persistently hot pixels are masked, an inconsistent merge triggers a retry at the measured beam centre, and builds targeting different CPU levels give the same results. * Rugnux: Improved scaling and merging - reflections with an overloaded pixel are dropped, as in XDS, sparse rotation sweeps are scaled more reliably, and French-Wilson amplitudes use an anisotropic Wilson prior. * Rugnux: Improved space-group determination - glide planes in groups without a centre of symmetry, screw axes from short or weak axial rows kept when a higher group is adopted, and more reliable decisions on twinned and pseudo-symmetric crystals. * Rugnux: Improved small-molecule processing - spots that grow wider than the integration disk and split spots are integrated over their measured footprint, sparse lattices are integrated on every frame, and the `.hkl` file holds unmerged scaled reflections (SHELX HKLF 4). * Rugnux: Reads Rigaku d*TREK SMV images (Saturn CCD), including detector 2theta and encoded pixel overflows; home-source (rotating-anode) datasets were added to the validation battery. * jfjoch_viewer: Fixed processing failing at the end with "Wrong JPEG library version" on Linux; the merge window shows the space group with proper subscripts and a checklist of crystal pathologies. Reviewed-on: #84 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-10-06 14:03:18 +02:00
leonarski_f	84228bf8be	v1.0.0-rc.173 (#83) ... * jfjoch_broker: Optional per-dataset authentication - statistics, images and plots can require a bearer token, which jfjoch_viewer supports. * jfjoch_viewer: Dark mode and a theme-matched colour scheme, a magnifier panel, and simpler contrast and background controls. * Rugnux: Multiple performance improvements on GPU and CPU (CPU-only processing up to 40% faster, faster image decoding on ARM), with unchanged results. * Rugnux: `--model` rigid-body refinement runs on the GPU, and the model-validation check is faster and more reliable. * Rugnux: Improved scaling and merging - error model, outlier rejection, absorption correction and French-Wilson amplitudes now agree more closely with XDS and ctruncate. * Rugnux: Improved integration - radial background on powder and ice rings, crowded rotation data keep their reflections, and CPU-only builds integrate large unit cells as GPU builds do. * Rugnux: More robust detector geometry - measured beam centre, X-ray bandwidth and goniometer rate, and geometry refinement accepted only on significant evidence. * Rugnux: Merged files are written in the standard setting, or in the setting of a reference MTZ, structure-factor mmCIF or model, with its free-R flags. * Rugnux: Richer report - ice and powder rings, further lattices, superstructure candidates and mosaicity, with warnings worded as prompts to check. * Rugnux: Clear error messages when a data set needs more GPU or host memory than is available. Reviewed-on: #83 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-29 15:57:32 +02:00