leonarski_fandClaude Opus 5.5
e4eaeba874
tools/battery/still/agipd_to_int16.py converts an AGIPD 1M Cheetah CXI file into the only form rugnux
supports for AGIPD: each module's eight 64-row ASICs placed 66 rows apart (the 2-pixel ASIC gaps
inserted), one 526 x 128 panel per module; the per-frame mask and mask_shared (bad bits = the
geometry's mask_bad) and the geometry's bad regions folded into the data as -32768; values
round(value / ADU per photon) as int16 (clipped to +-32767; no pixel clipped in either set);
bitshuffle/LZ4, one chunk per frame at /entry_1/data_1/data. It writes the matching CrystFEL geometry
(16 panels, each the rigid fit of its ASICs, module coffset kept) and refuses a module whose ASICs are
not on one straight line at a whole-pixel pitch within 0.5 px (worst here: 0.16 px for CXIDB 83,
0.002 px for 152).
Reader: a stored value equal to the smallest value of its signed integer type (INT16_MIN, INT32_MIN)
is no measurement. The reader decodes to float and divides by the gain, so -32768 used to come out as a
count; the CrystFEL parser takes only module geometry, so a flag_lessthan in the .geom could not say it.
Still battery: euxfel83 / euxfel152 read conv/*_int16.h5 with conv/agipd_int16.geom and --gain 1.
Full sets, -N 16, --refine-geometry=off, --model (other jobs on the machine, load 7-23):
indexed d_min CC1/2 CC_HALF_SPLIT R_split R_FREE main pass wall
CXIDB 83 original 90.9% 1.84 0.641 0.617 0.482 0.280 89.3 s (31/s) 105 s
converted 94.1% 1.84 0.686 0.644 0.470 0.277 6.5 s (429/s) 20 s
CXIDB 152 original 17.5% 5.37 0.521 0.479 0.590 0.308 131.7 s (29/s) 153 s
converted 62.8% 2.92 0.876 0.891 0.354 0.284 13.2 s (287/s) 27 s
Files 4.7 -> 1.3 GB and 5.7 -> 1.1 GB. The 152 gain is the mask: the reader took only Cheetah's
generic bad bits, while the geometry's mask_bad (0xffff) also marks three broken modules (bit 32) and
its bad region a fourth; the converter run with the generic bits instead gives 17.5% / 3.41 A again.
With geometry refinement on (16 rigid modules): 83 94.2%, 1.75 A, CC1/2 0.665, R_FREE 0.284, 49 s;
152 65.1%, 2.94 A, CC1/2 0.843, R_FREE 0.278, 27 s - mixed, the manifest keeps it off.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
Jungfraujoch
Application to receive and analyse data from the PSI JUNGFRAU and EIGER detectors, together with
rugnux, its program for processing stored diffraction data - rotation and serial, macromolecular
and small-molecule - from images to merged reflections.
All documentation is now placed in docs/ subdirectory and for the current version hosted on Jungfraujoch Read The Docs page.