Foreign stills files state their saturation level wrongly or not at all: an MPCCD Cheetah file is
dark-subtracted per pixel, so each pixel clips at the ADC limit less its own dark, and its
CrystFEL geometry leaves max_adu commented out - the run reported "Overloads: 0" while the inner
panels saturated in most frames.
saturation_ceiling (image_preprocessing/SaturationCeiling) histograms pixel values on a log
scale (64 bins per octave from 256) and returns the lower edge of the lowest bin holding over
twice what any of the 8 bins below it held (and at least 50 values): a bright tail only falls, a
clipped one piles up below where it stops, as a band where the level differs per pixel.
DetectSaturation runs it on 40 frames spread over every stills run and logs it beside the file's
limit; for any input but a Jungfraujoch-written file (ProcessConfig::detect_saturation) a level
below the file's replaces it. The CrystFEL/CXI reader, where the geometry states no max_adu, now
takes the stored integer type's maximum (an int16 Cheetah file clips at 32767).
The geometry-file-free CXI path (previous commit) is limited to square frames: a tiled detector's
Cheetah slab (CSPAD, AGIPD, MPCCD, ...) read as one flat panel would place every pixel wrongly
without a word, and those slabs are not square.
Measured:
MPCCD stills, 1339 frames: pile-up from 1218 photons (by hand 12000 ADU ~ 1200 ph); 5.5% of
reflections coarser than 4 A flagged; lowest-shell CC1/2 0.545 -> 0.674, overall 0.741 ->
0.793; same dimple refinement against the deposited model R-free 0.2586 -> 0.2556
single-panel Rayonix CXI, 1316 frames: no pile-up (20 pixels at the int16 limit in 40 frames);
the int16 limit flags 123 reflections; CC1/2 0.737 -> 0.787, rugnux R-free 0.382 -> 0.358
JUNGFRAU stills (Jungfraujoch files: lysozyme and two private sets): no pile-up below the stated
limit, results bit-identical
Cost 0.5 s per run.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
leonarski_fandClaude Opus 5.5
e4cb3e1b09