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
Every input is a file named on the command line, read in the order given (a shell glob gives them
sorted by name); a directory is refused with the glob form to use instead.
- Several Jungfraujoch/NXmx masters of stills are read as one run (JFJochMultiReader): their images
one after another, the pixel masks combined, the per-image efficiency placed at each input's
images. They must share the detector, wavelength (0.1%), distance (0.1 mm) and beam centre (1 px),
since stills geometry refinement refines one geometry for all frames; rotation sweeps are refused.
The log gives the indexing rate of each input beside the run's (ProcessResult::image_indexed).
- SACLA HDF5 / CXI (JFJochCrystFELReader::ReadFiles, ReadCXI, Open) and XTC
(JFJochXTCReader::ReadFiles) take the list of files instead of scanning a directory;
CanReadCXI and xtc::CanRead accept only a file; ListFiles and xtc::CollectStreams are gone.
- Several inputs must be one format, --mode mx, and stored files (no broker, no --simulate-live);
one frame of a CBF/marCCD/SMV sweep still names the whole sweep.
Validated: two Jungfraujoch lysozyme stills runs together (49,920 frames, known cell) 57.1% indexed (59.3% /
54.9% per run), 1.22 A, CC1/2 0.986, R_split 8.8%, REFMAC R/R-free 0.253/0.269 against 0.257/0.273
for the earlier hand-built combined master. Rotation: 5reo and lyso_x10sa_90deg_1 unchanged.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
Brings the stills-geom-auto-lcls merge resolution (b10a8ce00) onto the rc178-based stills branch.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
leonarski_fandClaude Opus 5.5