The .geom parser now takes the masking information the format defines:
- mask arrays: mask/mask_file/mask_good/mask_bad (mask 0) and maskN_data/maskN_file/maskN_goodbits/
maskN_badbits for N = 0..7; global keys hold for the panels after them, a panel may override. A mask
that is the same on every panel is one whole-frame mask, otherwise one per panel, applied on that
panel's pixels only.
- a relative mask_file is looked for in the working directory (as CrystFEL does), then beside the .geom.
- bad regions (bad*): a lab-plane box (min_x..max_y) or a fs/ss range on a panel (or, old syntax, on
the whole frame); mask_edge_pixels and no_index.
JFJochXFELReader already had the static pixel mask and the per-frame mask path for these; the masks
go through them unchanged. A mask whose path holds % (one per shot group) is applied frame by frame
like a 3D one. Where the geometry names mask arrays, the data file's own Cheetah masks (CXI
mask_shared and per-shot mask with Cheetah's generic bad bits, /metadata/pixelmask) are not added:
the geometry says which bits matter (e.g. an AGIPD mask_bad that includes bit 32). --mask-good /
--mask-bad still add their masks to these.
Tests: [CrystFELGeometry] (new keys, per-panel override, relative mask file), JFJochXFELReader_*
(new GeometryMasks case on a synthetic CXI + .geom), [JFJochMultiReader], JFJochXTCReader*.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
leonarski_fandClaude Opus 5.5
7c23b4befe
