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rugnux: background clip scaled by the CCD gain measured in the pre-scan

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The background ring's high-side clip, mean + 4*sqrt(mean), assumes counted photons. A CCD reports
ADU: on a Rigaku Saturn a background pixel scatters 4-5x its mean, so the clip sat at ~2 sigma, cut
the upper tail of every ring and added a positive offset to every reflection, compressing the
intensity statistics (a false 422 on one twinned I41 crystal).

No header carries a usable gain (SMV states none, every marCCD file the writer default of 1 ADU per
photon), so it is measured: background_gain::MeasureFrame takes the variance per unit mean of the
difference of pixels two columns apart, per level, clipped, on every fourth row of up to 16 of the
pre-scan's frames; Gain is the pair-weighted median over the levels. The clip becomes
mean + n*sqrt(max(g,1)*mean) (BraggIntegrationSettings::bkg_pixel_gain, CPU and GPU engines).
Only for SMV/marCCD input (ProcessConfig::counts_in_adu, set from the file format); HDF5 and CBF
keep g = 1, the identity. One log line reports the value. No new option.

Measured g: Saturn 944+ 4.7-5.2, Saturn 944 2.7, A200 0.68, ADSC ~0.3, marCCD ~0.3 - so the
ADSC/marCCD/A200 sets keep the photon clip exactly.

Checks (reflection data via gemmi and p.hkl, against the rc175 battery outputs / base build):
identical on 11if, 7qis, 8a1a, myob_x10sa, cytc_x10sa (photon counting), 4bwl, 5epe (ADSC,
marCCD) and 6cee (A200). Saturn sets, battery baseline -> this change:
  3r6o  I4122 R_meas 19.3% ISa 4.4 <|L|> .321 -> I41 (correct) 12.1% 8.1 .384
  3mc4  R_meas 10.2 -> 9.8 %, ISa 12.1 -> 12.7, d_min 1.79 -> 1.75 A, <|L|> .360 -> .391
  5uth  12.6 -> 11.8 %, ISa 10.4 -> 10.1, <|L|> .426 -> .483, offset vs |Fc|^2 0.21 -> 0.00
  5vml  10.2 -> 9.6 %, ISa 11.0 -> 11.6, <|L|> .426 -> .475, offset 0.15 -> 0.05
  5cc8  8.1 -> 7.9 %, ISa 10.8 -> 11.2, <|L|> .469 -> .494
  3meb  14.5 -> 14.6 %, ISa 13.2 -> 13.2, <|L|> .442 -> .457
Space groups unchanged except 3r6o. Pre-scan cost: +0.5 s on a 9 Mpx ADSC sweep, within noise on
a 15 Mpx marCCD sweep, nothing on HDF5/CBF.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi
This commit is contained in:
leonarski_f
2026-10-09 21:18:12 +02:00
co-authored by Claude Opus 5.5
parent e9d4f22210
commit aec6f6aabc
14 changed files with 313 additions and 4 deletions
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image_analysis/bragg_integration/BraggIntegrationEngineCPU.cpp
+4 -2
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@@ -311,8 +311,10 @@ std::vector<Reflection> BraggIntegrationEngineCPU::RunImpl(const Sampler &img,
}
} else if (do_clip) {
// One high-outlier sigma-clip pass on the background ring: reject pixels above
// mean + n*sqrt(mean) to strip a neighbour core or a zinger that biases the mean.
const double thr = out.bkg + bkg_clip_nsigma * std::sqrt(std::max(out.bkg, 1.0));
// mean + n*sqrt(gain*mean) to strip a neighbour core or a zinger that biases the mean.
// The gain is 1 for counted photons, so this is then exactly the Poisson clip.
const double thr = out.bkg + bkg_clip_nsigma * std::sqrt(static_cast<double>(bkg_pixel_gain)
* std::max(out.bkg, 1.0));
double s = 0.0;
int n = 0;
for (int y = y0; y <= y1; ++y)