3 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	a8202789f5	DetectorModules: panel look-up by id, plane -> panel, plane bounds and a per-pixel walk; mask size checked ... Stage 0 of analysing panel detectors in their stored layout. The table of modules already is the panel table; what the consumers converted in the next stages need from it: - ImageToPlane / PlaneToImage on a known panel, no search; panel -1 (empty table) is the identity. - PlaneToPanel: the panel holding a plane point and its image position, nullopt in a gap (never passed through, unlike the existing PlaneToImage). - PlaneBounds: the box of all panel footprints on the plane; with an empty table exactly the image rectangle today's prediction bounds test uses. - ForEachPixel: f(panel, index, px, py) panel by panel, row by row, gaps not visited; with an empty table the plain row-major loop with plane == image. The image preprocessors (CPU, GPU) and the Bragg engines (CPU, GPU; Metal derives from CPU) now refuse a pixel mask whose size is not the image's, instead of reading a mask of another size out of range. Every reader sizes the experiment's detector, and so the mask, by the image it reads, so nothing that runs today is refused. Nothing calls the new functions yet: no output changes. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu	2026-10-21 09:41:35 +02:00
leonarski_fandClaude Opus 5.5	b9ada7914b	DetectorModules.h: include <cstddef> for size_t ... GCC 12 (the Ubuntu 22.04 CI job) does not pull size_t in through <cstdint>/<vector>, so the header failed to compile there. Checked: all 601 project sources pass -fsyntax-only with GCC 12.2 (gcc-toolset-12). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu	2026-10-21 08:48:32 +02:00
leonarski_fandClaude Opus 5.5	ebce906025	Serial XFEL stills inputs: readers from the files themselves, module geometry and its refinement ... Combines the stills reader and module work (stills-readers, stills-modgeom, stills-euxfel) onto rc178 with the owner's decisions for this release: - Inputs are files, never a directory; several files of one format are one dataset (the multi-input CLI of the previous commit), so every reader takes an explicit list: JFJochXFELReader::ReadFiles, ReadCXI, ReadPanelTable and JFJochXTCReader::ReadFiles take std::vector<std::string>; ListFiles and xtc::CollectStreams are gone, CanRead* accept a regular file only. - One HDF5 frame reader (JFJochCrystFELReader -> JFJochXFELReader) parameterised by what the file holds: per-shot groups or a 3D stack, a /metadata panel table (posx/posy/angle, pixel size, nominal camera length, pixel mask: as SACLA writes), a Cheetah CXI single panel (square frame; a tiled slab is refused with a message). At most 8 files open; every file checked against the first. Signed 32-bit decode, per-frame 3D masks, panels at their own coffset (from the EuXFEL work). - Frames stored one chunk each are read the way the NXmx reader reads its images: only the chunk's place is asked of HDF5 under its lock (H5Dget_chunk_info_by_coord), the bytes are read through HDF5ImageSource::RawFile (positional, no lock) and decoded outside it - deflate(+shuffle) by zlib, bitshuffle/LZ4 (and zstd, plain LZ4) by CompressedImage's decoders. Bitshuffle/LZ4 used to go through HDF5's filter under the global lock, one frame at a time. - LCLS-I XTC (Rayonix): wavelength from the beam record, pixel size from the Rayonix model and binning, only --detector-distance needed; damaged/compressed frames skipped, a truncated last event dropped; std::ifstream, no POSIX calls: builds with MSVC. No DIALS .expt support at all. - CrystFEL .geom: module geometry only (panel ranges, fs/ss, corners, pixel size, coffset, data path) and optionally the camera length; everything else is ignored with a note in the log. - --mask-good / --mask-bad <file>:<dataset>: a mask array in another HDF5 file, in the frames' stored layout (what a .geom's mask_file used to give). - Gain measured on the background for panel-table and CXI input that states none (--gain overrides). - Detector modules from explicit geometry only (DetectorModules: the reader's panels, an NXmx file with one NXdetector_module per module, or --module-geometry); never from the image. Spots and predictions are mapped through the modules, the image is not re-assembled. - Module refinement in the stills bundle adjustment (Ceres; per-module shift and in-plane turn, gauge on mean shift/turn/scale and on the two tilt-like patterns when the tilt is refined; adopted only where it predicts held-out frames better). Applied for a foreign multi-panel detector (panel table, .geom panels); for a JUNGFRAU measured and reported only. Written to <prefix>_modules.h5 (NXmx NXdetector_module groups), read back with --module-geometry. - A panel-table file's camera length is nominal: with a reference cell it is refined from the cell. - Broker and writer output unchanged: masters keep the single NXdetector_module group, the start message carries no module list. Tests: [CrystFELGeometry], JFJochXFELReader_*, JFJochXTCReader, [JFJochMultiReader], [CellPopulation], SaturationCeiling_*, [DetectorModules], RefineGlobalGeometry_ModulePlacement, [reindex], Sublattice. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu	2026-10-20 23:30:48 +02:00