A CrystFEL .geom (current and old syntax) is parsed for panels (pixel ranges, fs/ss, corners),
clen/coffset (a number, or an HDF5 path read as mm), res, adu_per_eV/adu_per_photon, max_adu,
no_index, bad regions (panel, whole-frame or lab-plane) and the HDF5 mask (mask/mask_file,
mask_good/mask_bad). JFJochCrystFELReader reads the frames the geometry's data path names - a 3D
stack (Cheetah CXI), one 2D frame per file, or one group per shot (/%/data) - from a file or a
directory, puts the panels on one flat image at their rounded positions with gaps and bad regions
masked, and converts to photons where a gain is stated (otherwise the pre-scan measures it). One
wavelength and one camera length per run: values taken from the files are averaged over the first
file. Panel positions are used as given. Frames stored as one deflate(+shuffle) chunk are read raw
under the HDF5 lock and decoded outside it.
Replaces the MPCCD-specific reader of the previous commit.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
leonarski_fandClaude Opus 5.5
ce528f3a14