A component of more than 50 connected pixels was discarded. Under the
self-calibrating threshold that is an INTENSITY CEILING, not a size bound: the
threshold is an absolute per-ring contour, so a component's area above it grows
as sigma^2*ln(A/T), without bound in the peak amplitude. Measured on the strong
rotation set, footprints run 3 px at 30-100 counts to 50 px above 10000 - a
slope of 4.4 px per ln(peak) against the fixed local-box test's 0.8, which
saturates at 13 px and never reaches the bound at all. So the brighter a
reflection, the more certainly it was thrown away: 59% of the box finder's
d>3 A spots were missing from the adaptive finder's list, including every one
of its ten strongest, at an intensity ratio of 1.085 for those that did match.
Indexed spots per image collapsed from 220 to 7.
Raise the bound to 200 - CrystFEL peakfinder8's --max-pix-count, the only
directly comparable number in the field; XDS has no such parameter and guards
on shape instead - and ask a component above 50 pixels to be COMPACT: it must
fill a fifth of the square its bounding box fits inside. A Bragg reflection is
round and fills about half of that square however bright it is; an ice arc, a
cosmic-ray track or a lit detector row fills a fifth or less, and those are what
an upper bound was ever protecting against. Below 50 nothing is asked of the
shape, so every component accepted before still is. Integer arithmetic on both
sides, and on the GPU the bounding side fits in what was padding, so the device
struct does not grow.
The shape test is what makes the raise safe. With a flat 200 alone, two battery
crystals moved: one lost a little I/sigma, and the other's de-novo lattice was
NOT MONOTONE in the bound - correct at 50, 100 and 200, wrong at 150 and at 250
and above - so 200 was partly luck. With the shape test both are unchanged to
three decimals.
De novo at defaults on the strong set: indexing rate 0.574 -> 0.804,
completeness 97.3 -> 99.6%, <I/sigma> 3.42 -> 6.07, R_meas 0.299 -> 0.249,
CC1/2 0.947 -> 0.961, ISa 3.29 -> 4.13. The full 37-crystal battery, scored per
shell, is still owed.
Also documents what StrongPixelSet::AddStrongPixel has required since the
component search became linear - pixels in raster order - and puts the existing
test's insertion order into it. Both callers scan a bitmap in ascending flat
index and always satisfied it; the test did not, and was the only thing that
did not.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FBumeJVx4oeXxiBRpkrE5H
This is an UNSTABLE release and not recommended for production use (please use rc.96 instead).
* jfjoch_broker: For DECTRIS detectors add dark data collection during initialization for bad pixel mask
* jfjoch_broker: Refactor of calibration logic for more clear code (likely to introduce problems)
* jfjoch_viewer: Add option to handle user pixel mask (experimental)
* jfjoch_viewer: More options for ROI
* jfjoch_viewer: Add window to display calibration
Reviewed-on: #2
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
leonarski_fandClaude Opus 5